Back to the "Multiple platform build/check report"

Package 92/188OSArchBUILDCHECKBUILD BIN

limma

2.8.1

Gordon Smyth
Linux (SUSE 9.2) x86_64 OK  OK 
Linux (SUSE 9.2) i686 OK [ OK ]
Solaris 2.9 sparc OK  OK 
Windows Server 2003 x86_64 OK  OK  OK 
Package: limma
Version: 2.8.1
Command: /loc/biocbuild/1.9d/R/bin/R CMD check limma_2.8.1.tar.gz
RetCode: 0
Time: 254.6 seconds
Status: OK
CheckDir: limma.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/1.9d/Rpacks/limma.Rcheck'
* using R version 2.4.0 (2006-10-03)
* checking for file 'limma/DESCRIPTION' ... OK
* this is package 'limma' version '2.8.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'limma' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating limma-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/extra/loc/biocbuild/1.9d/Rpacks/limma.Rcheck/tests'
  Running 'limma-Tests.R'
  Comparing 'limma-Tests.Rout' to 'limma-Tests.Rout.save' ...2,933d1
< 
< > library(limma)
< > 
< > set.seed(0); u <- runif(100)
< > 
< > ### splitName
< > 
< > x <- c("ab;cd;efg","abc;def","z","")
< > splitName(x)
< $Name
< [1] "ab;cd" "abc"   "z"     ""     
< 
< $Annotation
< [1] "efg" "def" ""    ""   
< 
< > 
< > ### removeext
< > 
< > removeExt(c("slide1.spot","slide.2.spot"))
< [1] "slide1"  "slide.2"
< > removeExt(c("slide1.spot","slide"))
< [1] "slide1.spot" "slide"      
< > 
< > ### printorder
< > printorder(list(ngrid.r=4,ngrid.c=4,nspot.r=8,nspot.c=6),ndups=2,start="topright",npins=4)
< $printorder
<   [1]   6   5   4   3   2   1  12  11  10   9   8   7  18  17  16  15  14  13
<  [19]  24  23  22  21  20  19  30  29  28  27  26  25  36  35  34  33  32  31
<  [37]  42  41  40  39  38  37  48  47  46  45  44  43   6   5   4   3   2   1
<  [55]  12  11  10   9   8   7  18  17  16  15  14  13  24  23  22  21  20  19
<  [73]  30  29  28  27  26  25  36  35  34  33  32  31  42  41  40  39  38  37
<  [91]  48  47  46  45  44  43   6   5   4   3   2   1  12  11  10   9   8   7
< [109]  18  17  16  15  14  13  24  23  22  21  20  19  30  29  28  27  26  25
< [127]  36  35  34  33  32  31  42  41  40  39  38  37  48  47  46  45  44  43
< [145]   6   5   4   3   2   1  12  11  10   9   8   7  18  17  16  15  14  13
< [163]  24  23  22  21  20  19  30  29  28  27  26  25  36  35  34  33  32  31
< [181]  42  41  40  39  38  37  48  47  46  45  44  43  54  53  52  51  50  49
< [199]  60  59  58  57  56  55  66  65  64  63  62  61  72  71  70  69  68  67
< [217]  78  77  76  75  74  73  84  83  82  81  80  79  90  89  88  87  86  85
< [235]  96  95  94  93  92  91  54  53  52  51  50  49  60  59  58  57  56  55
< [253]  66  65  64  63  62  61  72  71  70  69  68  67  78  77  76  75  74  73
< [271]  84  83  82  81  80  79  90  89  88  87  86  85  96  95  94  93  92  91
< [289]  54  53  52  51  50  49  60  59  58  57  56  55  66  65  64  63  62  61
< [307]  72  71  70  69  68  67  78  77  76  75  74  73  84  83  82  81  80  79
< [325]  90  89  88  87  86  85  96  95  94  93  92  91  54  53  52  51  50  49
< [343]  60  59  58  57  56  55  66  65  64  63  62  61  72  71  70  69  68  67
< [361]  78  77  76  75  74  73  84  83  82  81  80  79  90  89  88  87  86  85
< [379]  96  95  94  93  92  91 102 101 100  99  98  97 108 107 106 105 104 103
< [397] 114 113 112 111 110 109 120 119 118 117 116 115 126 125 124 123 122 121
< [415] 132 131 130 129 128 127 138 137 136 135 134 133 144 143 142 141 140 139
< [433] 102 101 100  99  98  97 108 107 106 105 104 103 114 113 112 111 110 109
< [451] 120 119 118 117 116 115 126 125 124 123 122 121 132 131 130 129 128 127
< [469] 138 137 136 135 134 133 144 143 142 141 140 139 102 101 100  99  98  97
< [487] 108 107 106 105 104 103 114 113 112 111 110 109 120 119 118 117 116 115
< [505] 126 125 124 123 122 121 132 131 130 129 128 127 138 137 136 135 134 133
< [523] 144 143 142 141 140 139 102 101 100  99  98  97 108 107 106 105 104 103
< [541] 114 113 112 111 110 109 120 119 118 117 116 115 126 125 124 123 122 121
< [559] 132 131 130 129 128 127 138 137 136 135 134 133 144 143 142 141 140 139
< [577] 150 149 148 147 146 145 156 155 154 153 152 151 162 161 160 159 158 157
< [595] 168 167 166 165 164 163 174 173 172 171 170 169 180 179 178 177 176 175
< [613] 186 185 184 183 182 181 192 191 190 189 188 187 150 149 148 147 146 145
< [631] 156 155 154 153 152 151 162 161 160 159 158 157 168 167 166 165 164 163
< [649] 174 173 172 171 170 169 180 179 178 177 176 175 186 185 184 183 182 181
< [667] 192 191 190 189 188 187 150 149 148 147 146 145 156 155 154 153 152 151
< [685] 162 161 160 159 158 157 168 167 166 165 164 163 174 173 172 171 170 169
< [703] 180 179 178 177 176 175 186 185 184 183 182 181 192 191 190 189 188 187
< [721] 150 149 148 147 146 145 156 155 154 153 152 151 162 161 160 159 158 157
< [739] 168 167 166 165 164 163 174 173 172 171 170 169 180 179 178 177 176 175
< [757] 186 185 184 183 182 181 192 191 190 189 188 187
< 
< $plate
<   [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
<  [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
<  [75] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [112] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [149] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [186] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [223] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [260] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [297] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [334] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [371] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [408] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [445] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [482] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [519] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [556] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [593] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [630] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [667] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [704] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [741] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< 
< $plate.r
<   [1]  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4
<  [26]  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  4  3  3
<  [51]  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3
<  [76]  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  3  2  2  2  2
< [101]  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2
< [126]  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  1  1  1  1  1  1
< [151]  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1
< [176]  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  8  8  8  8  8  8  8  8
< [201]  8  8  8  8  8  8  8  8  8  8  8  8  8  8  8  8  8  8  8  8  8  8  8  8  8
< [226]  8  8  8  8  8  8  8  8  8  8  8  8  8  8  8  7  7  7  7  7  7  7  7  7  7
< [251]  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7
< [276]  7  7  7  7  7  7  7  7  7  7  7  7  7  6  6  6  6  6  6  6  6  6  6  6  6
< [301]  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6  6
< [326]  6  6  6  6  6  6  6  6  6  6  6  5  5  5  5  5  5  5  5  5  5  5  5  5  5
< [351]  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5  5
< [376]  5  5  5  5  5  5  5  5  5 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12
< [401] 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12
< [426] 12 12 12 12 12 12 12 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11
< [451] 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11
< [476] 11 11 11 11 11 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10
< [501] 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10
< [526] 10 10 10  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9
< [551]  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9  9
< [576]  9 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16
< [601] 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 15
< [626] 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15
< [651] 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 14 14 14
< [676] 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14
< [701] 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 13 13 13 13 13
< [726] 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13
< [751] 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13
< 
< $plate.c
<   [1]  3  3  2  2  1  1  6  6  5  5  4  4  9  9  8  8  7  7 12 12 11 11 10 10 15
<  [26] 15 14 14 13 13 18 18 17 17 16 16 21 21 20 20 19 19 24 24 23 23 22 22  3  3
<  [51]  2  2  1  1  6  6  5  5  4  4  9  9  8  8  7  7 12 12 11 11 10 10 15 15 14
<  [76] 14 13 13 18 18 17 17 16 16 21 21 20 20 19 19 24 24 23 23 22 22  3  3  2  2
< [101]  1  1  6  6  5  5  4  4  9  9  8  8  7  7 12 12 11 11 10 10 15 15 14 14 13
< [126] 13 18 18 17 17 16 16 21 21 20 20 19 19 24 24 23 23 22 22  3  3  2  2  1  1
< [151]  6  6  5  5  4  4  9  9  8  8  7  7 12 12 11 11 10 10 15 15 14 14 13 13 18
< [176] 18 17 17 16 16 21 21 20 20 19 19 24 24 23 23 22 22  3  3  2  2  1  1  6  6
< [201]  5  5  4  4  9  9  8  8  7  7 12 12 11 11 10 10 15 15 14 14 13 13 18 18 17
< [226] 17 16 16 21 21 20 20 19 19 24 24 23 23 22 22  3  3  2  2  1  1  6  6  5  5
< [251]  4  4  9  9  8  8  7  7 12 12 11 11 10 10 15 15 14 14 13 13 18 18 17 17 16
< [276] 16 21 21 20 20 19 19 24 24 23 23 22 22  3  3  2  2  1  1  6  6  5  5  4  4
< [301]  9  9  8  8  7  7 12 12 11 11 10 10 15 15 14 14 13 13 18 18 17 17 16 16 21
< [326] 21 20 20 19 19 24 24 23 23 22 22  3  3  2  2  1  1  6  6  5  5  4  4  9  9
< [351]  8  8  7  7 12 12 11 11 10 10 15 15 14 14 13 13 18 18 17 17 16 16 21 21 20
< [376] 20 19 19 24 24 23 23 22 22  3  3  2  2  1  1  6  6  5  5  4  4  9  9  8  8
< [401]  7  7 12 12 11 11 10 10 15 15 14 14 13 13 18 18 17 17 16 16 21 21 20 20 19
< [426] 19 24 24 23 23 22 22  3  3  2  2  1  1  6  6  5  5  4  4  9  9  8  8  7  7
< [451] 12 12 11 11 10 10 15 15 14 14 13 13 18 18 17 17 16 16 21 21 20 20 19 19 24
< [476] 24 23 23 22 22  3  3  2  2  1  1  6  6  5  5  4  4  9  9  8  8  7  7 12 12
< [501] 11 11 10 10 15 15 14 14 13 13 18 18 17 17 16 16 21 21 20 20 19 19 24 24 23
< [526] 23 22 22  3  3  2  2  1  1  6  6  5  5  4  4  9  9  8  8  7  7 12 12 11 11
< [551] 10 10 15 15 14 14 13 13 18 18 17 17 16 16 21 21 20 20 19 19 24 24 23 23 22
< [576] 22  3  3  2  2  1  1  6  6  5  5  4  4  9  9  8  8  7  7 12 12 11 11 10 10
< [601] 15 15 14 14 13 13 18 18 17 17 16 16 21 21 20 20 19 19 24 24 23 23 22 22  3
< [626]  3  2  2  1  1  6  6  5  5  4  4  9  9  8  8  7  7 12 12 11 11 10 10 15 15
< [651] 14 14 13 13 18 18 17 17 16 16 21 21 20 20 19 19 24 24 23 23 22 22  3  3  2
< [676]  2  1  1  6  6  5  5  4  4  9  9  8  8  7  7 12 12 11 11 10 10 15 15 14 14
< [701] 13 13 18 18 17 17 16 16 21 21 20 20 19 19 24 24 23 23 22 22  3  3  2  2  1
< [726]  1  6  6  5  5  4  4  9  9  8  8  7  7 12 12 11 11 10 10 15 15 14 14 13 13
< [751] 18 18 17 17 16 16 21 21 20 20 19 19 24 24 23 23 22 22
< 
< $plateposition
<   [1] "p1D03" "p1D03" "p1D02" "p1D02" "p1D01" "p1D01" "p1D06" "p1D06" "p1D05"
<  [10] "p1D05" "p1D04" "p1D04" "p1D09" "p1D09" "p1D08" "p1D08" "p1D07" "p1D07"
<  [19] "p1D12" "p1D12" "p1D11" "p1D11" "p1D10" "p1D10" "p1D15" "p1D15" "p1D14"
<  [28] "p1D14" "p1D13" "p1D13" "p1D18" "p1D18" "p1D17" "p1D17" "p1D16" "p1D16"
<  [37] "p1D21" "p1D21" "p1D20" "p1D20" "p1D19" "p1D19" "p1D24" "p1D24" "p1D23"
<  [46] "p1D23" "p1D22" "p1D22" "p1C03" "p1C03" "p1C02" "p1C02" "p1C01" "p1C01"
<  [55] "p1C06" "p1C06" "p1C05" "p1C05" "p1C04" "p1C04" "p1C09" "p1C09" "p1C08"
<  [64] "p1C08" "p1C07" "p1C07" "p1C12" "p1C12" "p1C11" "p1C11" "p1C10" "p1C10"
<  [73] "p1C15" "p1C15" "p1C14" "p1C14" "p1C13" "p1C13" "p1C18" "p1C18" "p1C17"
<  [82] "p1C17" "p1C16" "p1C16" "p1C21" "p1C21" "p1C20" "p1C20" "p1C19" "p1C19"
<  [91] "p1C24" "p1C24" "p1C23" "p1C23" "p1C22" "p1C22" "p1B03" "p1B03" "p1B02"
< [100] "p1B02" "p1B01" "p1B01" "p1B06" "p1B06" "p1B05" "p1B05" "p1B04" "p1B04"
< [109] "p1B09" "p1B09" "p1B08" "p1B08" "p1B07" "p1B07" "p1B12" "p1B12" "p1B11"
< [118] "p1B11" "p1B10" "p1B10" "p1B15" "p1B15" "p1B14" "p1B14" "p1B13" "p1B13"
< [127] "p1B18" "p1B18" "p1B17" "p1B17" "p1B16" "p1B16" "p1B21" "p1B21" "p1B20"
< [136] "p1B20" "p1B19" "p1B19" "p1B24" "p1B24" "p1B23" "p1B23" "p1B22" "p1B22"
< [145] "p1A03" "p1A03" "p1A02" "p1A02" "p1A01" "p1A01" "p1A06" "p1A06" "p1A05"
< [154] "p1A05" "p1A04" "p1A04" "p1A09" "p1A09" "p1A08" "p1A08" "p1A07" "p1A07"
< [163] "p1A12" "p1A12" "p1A11" "p1A11" "p1A10" "p1A10" "p1A15" "p1A15" "p1A14"
< [172] "p1A14" "p1A13" "p1A13" "p1A18" "p1A18" "p1A17" "p1A17" "p1A16" "p1A16"
< [181] "p1A21" "p1A21" "p1A20" "p1A20" "p1A19" "p1A19" "p1A24" "p1A24" "p1A23"
< [190] "p1A23" "p1A22" "p1A22" "p1H03" "p1H03" "p1H02" "p1H02" "p1H01" "p1H01"
< [199] "p1H06" "p1H06" "p1H05" "p1H05" "p1H04" "p1H04" "p1H09" "p1H09" "p1H08"
< [208] "p1H08" "p1H07" "p1H07" "p1H12" "p1H12" "p1H11" "p1H11" "p1H10" "p1H10"
< [217] "p1H15" "p1H15" "p1H14" "p1H14" "p1H13" "p1H13" "p1H18" "p1H18" "p1H17"
< [226] "p1H17" "p1H16" "p1H16" "p1H21" "p1H21" "p1H20" "p1H20" "p1H19" "p1H19"
< [235] "p1H24" "p1H24" "p1H23" "p1H23" "p1H22" "p1H22" "p1G03" "p1G03" "p1G02"
< [244] "p1G02" "p1G01" "p1G01" "p1G06" "p1G06" "p1G05" "p1G05" "p1G04" "p1G04"
< [253] "p1G09" "p1G09" "p1G08" "p1G08" "p1G07" "p1G07" "p1G12" "p1G12" "p1G11"
< [262] "p1G11" "p1G10" "p1G10" "p1G15" "p1G15" "p1G14" "p1G14" "p1G13" "p1G13"
< [271] "p1G18" "p1G18" "p1G17" "p1G17" "p1G16" "p1G16" "p1G21" "p1G21" "p1G20"
< [280] "p1G20" "p1G19" "p1G19" "p1G24" "p1G24" "p1G23" "p1G23" "p1G22" "p1G22"
< [289] "p1F03" "p1F03" "p1F02" "p1F02" "p1F01" "p1F01" "p1F06" "p1F06" "p1F05"
< [298] "p1F05" "p1F04" "p1F04" "p1F09" "p1F09" "p1F08" "p1F08" "p1F07" "p1F07"
< [307] "p1F12" "p1F12" "p1F11" "p1F11" "p1F10" "p1F10" "p1F15" "p1F15" "p1F14"
< [316] "p1F14" "p1F13" "p1F13" "p1F18" "p1F18" "p1F17" "p1F17" "p1F16" "p1F16"
< [325] "p1F21" "p1F21" "p1F20" "p1F20" "p1F19" "p1F19" "p1F24" "p1F24" "p1F23"
< [334] "p1F23" "p1F22" "p1F22" "p1E03" "p1E03" "p1E02" "p1E02" "p1E01" "p1E01"
< [343] "p1E06" "p1E06" "p1E05" "p1E05" "p1E04" "p1E04" "p1E09" "p1E09" "p1E08"
< [352] "p1E08" "p1E07" "p1E07" "p1E12" "p1E12" "p1E11" "p1E11" "p1E10" "p1E10"
< [361] "p1E15" "p1E15" "p1E14" "p1E14" "p1E13" "p1E13" "p1E18" "p1E18" "p1E17"
< [370] "p1E17" "p1E16" "p1E16" "p1E21" "p1E21" "p1E20" "p1E20" "p1E19" "p1E19"
< [379] "p1E24" "p1E24" "p1E23" "p1E23" "p1E22" "p1E22" "p1L03" "p1L03" "p1L02"
< [388] "p1L02" "p1L01" "p1L01" "p1L06" "p1L06" "p1L05" "p1L05" "p1L04" "p1L04"
< [397] "p1L09" "p1L09" "p1L08" "p1L08" "p1L07" "p1L07" "p1L12" "p1L12" "p1L11"
< [406] "p1L11" "p1L10" "p1L10" "p1L15" "p1L15" "p1L14" "p1L14" "p1L13" "p1L13"
< [415] "p1L18" "p1L18" "p1L17" "p1L17" "p1L16" "p1L16" "p1L21" "p1L21" "p1L20"
< [424] "p1L20" "p1L19" "p1L19" "p1L24" "p1L24" "p1L23" "p1L23" "p1L22" "p1L22"
< [433] "p1K03" "p1K03" "p1K02" "p1K02" "p1K01" "p1K01" "p1K06" "p1K06" "p1K05"
< [442] "p1K05" "p1K04" "p1K04" "p1K09" "p1K09" "p1K08" "p1K08" "p1K07" "p1K07"
< [451] "p1K12" "p1K12" "p1K11" "p1K11" "p1K10" "p1K10" "p1K15" "p1K15" "p1K14"
< [460] "p1K14" "p1K13" "p1K13" "p1K18" "p1K18" "p1K17" "p1K17" "p1K16" "p1K16"
< [469] "p1K21" "p1K21" "p1K20" "p1K20" "p1K19" "p1K19" "p1K24" "p1K24" "p1K23"
< [478] "p1K23" "p1K22" "p1K22" "p1J03" "p1J03" "p1J02" "p1J02" "p1J01" "p1J01"
< [487] "p1J06" "p1J06" "p1J05" "p1J05" "p1J04" "p1J04" "p1J09" "p1J09" "p1J08"
< [496] "p1J08" "p1J07" "p1J07" "p1J12" "p1J12" "p1J11" "p1J11" "p1J10" "p1J10"
< [505] "p1J15" "p1J15" "p1J14" "p1J14" "p1J13" "p1J13" "p1J18" "p1J18" "p1J17"
< [514] "p1J17" "p1J16" "p1J16" "p1J21" "p1J21" "p1J20" "p1J20" "p1J19" "p1J19"
< [523] "p1J24" "p1J24" "p1J23" "p1J23" "p1J22" "p1J22" "p1I03" "p1I03" "p1I02"
< [532] "p1I02" "p1I01" "p1I01" "p1I06" "p1I06" "p1I05" "p1I05" "p1I04" "p1I04"
< [541] "p1I09" "p1I09" "p1I08" "p1I08" "p1I07" "p1I07" "p1I12" "p1I12" "p1I11"
< [550] "p1I11" "p1I10" "p1I10" "p1I15" "p1I15" "p1I14" "p1I14" "p1I13" "p1I13"
< [559] "p1I18" "p1I18" "p1I17" "p1I17" "p1I16" "p1I16" "p1I21" "p1I21" "p1I20"
< [568] "p1I20" "p1I19" "p1I19" "p1I24" "p1I24" "p1I23" "p1I23" "p1I22" "p1I22"
< [577] "p1P03" "p1P03" "p1P02" "p1P02" "p1P01" "p1P01" "p1P06" "p1P06" "p1P05"
< [586] "p1P05" "p1P04" "p1P04" "p1P09" "p1P09" "p1P08" "p1P08" "p1P07" "p1P07"
< [595] "p1P12" "p1P12" "p1P11" "p1P11" "p1P10" "p1P10" "p1P15" "p1P15" "p1P14"
< [604] "p1P14" "p1P13" "p1P13" "p1P18" "p1P18" "p1P17" "p1P17" "p1P16" "p1P16"
< [613] "p1P21" "p1P21" "p1P20" "p1P20" "p1P19" "p1P19" "p1P24" "p1P24" "p1P23"
< [622] "p1P23" "p1P22" "p1P22" "p1O03" "p1O03" "p1O02" "p1O02" "p1O01" "p1O01"
< [631] "p1O06" "p1O06" "p1O05" "p1O05" "p1O04" "p1O04" "p1O09" "p1O09" "p1O08"
< [640] "p1O08" "p1O07" "p1O07" "p1O12" "p1O12" "p1O11" "p1O11" "p1O10" "p1O10"
< [649] "p1O15" "p1O15" "p1O14" "p1O14" "p1O13" "p1O13" "p1O18" "p1O18" "p1O17"
< [658] "p1O17" "p1O16" "p1O16" "p1O21" "p1O21" "p1O20" "p1O20" "p1O19" "p1O19"
< [667] "p1O24" "p1O24" "p1O23" "p1O23" "p1O22" "p1O22" "p1N03" "p1N03" "p1N02"
< [676] "p1N02" "p1N01" "p1N01" "p1N06" "p1N06" "p1N05" "p1N05" "p1N04" "p1N04"
< [685] "p1N09" "p1N09" "p1N08" "p1N08" "p1N07" "p1N07" "p1N12" "p1N12" "p1N11"
< [694] "p1N11" "p1N10" "p1N10" "p1N15" "p1N15" "p1N14" "p1N14" "p1N13" "p1N13"
< [703] "p1N18" "p1N18" "p1N17" "p1N17" "p1N16" "p1N16" "p1N21" "p1N21" "p1N20"
< [712] "p1N20" "p1N19" "p1N19" "p1N24" "p1N24" "p1N23" "p1N23" "p1N22" "p1N22"
< [721] "p1M03" "p1M03" "p1M02" "p1M02" "p1M01" "p1M01" "p1M06" "p1M06" "p1M05"
< [730] "p1M05" "p1M04" "p1M04" "p1M09" "p1M09" "p1M08" "p1M08" "p1M07" "p1M07"
< [739] "p1M12" "p1M12" "p1M11" "p1M11" "p1M10" "p1M10" "p1M15" "p1M15" "p1M14"
< [748] "p1M14" "p1M13" "p1M13" "p1M18" "p1M18" "p1M17" "p1M17" "p1M16" "p1M16"
< [757] "p1M21" "p1M21" "p1M20" "p1M20" "p1M19" "p1M19" "p1M24" "p1M24" "p1M23"
< [766] "p1M23" "p1M22" "p1M22"
< 
< > printorder(list(ngrid.r=4,ngrid.c=4,nspot.r=8,nspot.c=6))
< $printorder
<   [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
<  [26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48  1  2
<  [51]  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27
<  [76] 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48  1  2  3  4
< [101]  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29
< [126] 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48  1  2  3  4  5  6
< [151]  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31
< [176] 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48  1  2  3  4  5  6  7  8
< [201]  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33
< [226] 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48  1  2  3  4  5  6  7  8  9 10
< [251] 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35
< [276] 36 37 38 39 40 41 42 43 44 45 46 47 48  1  2  3  4  5  6  7  8  9 10 11 12
< [301] 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37
< [326] 38 39 40 41 42 43 44 45 46 47 48  1  2  3  4  5  6  7  8  9 10 11 12 13 14
< [351] 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
< [376] 40 41 42 43 44 45 46 47 48  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16
< [401] 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41
< [426] 42 43 44 45 46 47 48  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18
< [451] 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43
< [476] 44 45 46 47 48  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20
< [501] 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
< [526] 46 47 48  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22
< [551] 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47
< [576] 48  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
< [601] 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48  1
< [626]  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
< [651] 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48  1  2  3
< [676]  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
< [701] 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48  1  2  3  4  5
< [726]  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
< [751] 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
< 
< $plate
<   [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2
<  [38] 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2
<  [75] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [112] 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1
< [149] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
< [186] 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2
< [223] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [260] 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1
< [297] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
< [334] 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2
< [371] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [408] 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1
< [445] 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1
< [482] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2
< [519] 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2
< [556] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [593] 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1
< [630] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
< [667] 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2
< [704] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
< [741] 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
< 
< $plate.r
<   [1]  4  4  4  4  4  4  8  8  8  8  8  8 12 12 12 12 12 12 16 16 16 16 16 16  4
<  [26]  4  4  4  4  4  8  8  8  8  8  8 12 12 12 12 12 12 16 16 16 16 16 16  3  3
<  [51]  3  3  3  3  7  7  7  7  7  7 11 11 11 11 11 11 15 15 15 15 15 15  3  3  3
<  [76]  3  3  3  7  7  7  7  7  7 11 11 11 11 11 11 15 15 15 15 15 15  2  2  2  2
< [101]  2  2  6  6  6  6  6  6 10 10 10 10 10 10 14 14 14 14 14 14  2  2  2  2  2
< [126]  2  6  6  6  6  6  6 10 10 10 10 10 10 14 14 14 14 14 14  1  1  1  1  1  1
< [151]  5  5  5  5  5  5  9  9  9  9  9  9 13 13 13 13 13 13  1  1  1  1  1  1  5
< [176]  5  5  5  5  5  9  9  9  9  9  9 13 13 13 13 13 13  4  4  4  4  4  4  8  8
< [201]  8  8  8  8 12 12 12 12 12 12 16 16 16 16 16 16  4  4  4  4  4  4  8  8  8
< [226]  8  8  8 12 12 12 12 12 12 16 16 16 16 16 16  3  3  3  3  3  3  7  7  7  7
< [251]  7  7 11 11 11 11 11 11 15 15 15 15 15 15  3  3  3  3  3  3  7  7  7  7  7
< [276]  7 11 11 11 11 11 11 15 15 15 15 15 15  2  2  2  2  2  2  6  6  6  6  6  6
< [301] 10 10 10 10 10 10 14 14 14 14 14 14  2  2  2  2  2  2  6  6  6  6  6  6 10
< [326] 10 10 10 10 10 14 14 14 14 14 14  1  1  1  1  1  1  5  5  5  5  5  5  9  9
< [351]  9  9  9  9 13 13 13 13 13 13  1  1  1  1  1  1  5  5  5  5  5  5  9  9  9
< [376]  9  9  9 13 13 13 13 13 13  4  4  4  4  4  4  8  8  8  8  8  8 12 12 12 12
< [401] 12 12 16 16 16 16 16 16  4  4  4  4  4  4  8  8  8  8  8  8 12 12 12 12 12
< [426] 12 16 16 16 16 16 16  3  3  3  3  3  3  7  7  7  7  7  7 11 11 11 11 11 11
< [451] 15 15 15 15 15 15  3  3  3  3  3  3  7  7  7  7  7  7 11 11 11 11 11 11 15
< [476] 15 15 15 15 15  2  2  2  2  2  2  6  6  6  6  6  6 10 10 10 10 10 10 14 14
< [501] 14 14 14 14  2  2  2  2  2  2  6  6  6  6  6  6 10 10 10 10 10 10 14 14 14
< [526] 14 14 14  1  1  1  1  1  1  5  5  5  5  5  5  9  9  9  9  9  9 13 13 13 13
< [551] 13 13  1  1  1  1  1  1  5  5  5  5  5  5  9  9  9  9  9  9 13 13 13 13 13
< [576] 13  4  4  4  4  4  4  8  8  8  8  8  8 12 12 12 12 12 12 16 16 16 16 16 16
< [601]  4  4  4  4  4  4  8  8  8  8  8  8 12 12 12 12 12 12 16 16 16 16 16 16  3
< [626]  3  3  3  3  3  7  7  7  7  7  7 11 11 11 11 11 11 15 15 15 15 15 15  3  3
< [651]  3  3  3  3  7  7  7  7  7  7 11 11 11 11 11 11 15 15 15 15 15 15  2  2  2
< [676]  2  2  2  6  6  6  6  6  6 10 10 10 10 10 10 14 14 14 14 14 14  2  2  2  2
< [701]  2  2  6  6  6  6  6  6 10 10 10 10 10 10 14 14 14 14 14 14  1  1  1  1  1
< [726]  1  5  5  5  5  5  5  9  9  9  9  9  9 13 13 13 13 13 13  1  1  1  1  1  1
< [751]  5  5  5  5  5  5  9  9  9  9  9  9 13 13 13 13 13 13
< 
< $plate.c
<   [1]  1  5  9 13 17 21  1  5  9 13 17 21  1  5  9 13 17 21  1  5  9 13 17 21  1
<  [26]  5  9 13 17 21  1  5  9 13 17 21  1  5  9 13 17 21  1  5  9 13 17 21  1  5
<  [51]  9 13 17 21  1  5  9 13 17 21  1  5  9 13 17 21  1  5  9 13 17 21  1  5  9
<  [76] 13 17 21  1  5  9 13 17 21  1  5  9 13 17 21  1  5  9 13 17 21  1  5  9 13
< [101] 17 21  1  5  9 13 17 21  1  5  9 13 17 21  1  5  9 13 17 21  1  5  9 13 17
< [126] 21  1  5  9 13 17 21  1  5  9 13 17 21  1  5  9 13 17 21  1  5  9 13 17 21
< [151]  1  5  9 13 17 21  1  5  9 13 17 21  1  5  9 13 17 21  1  5  9 13 17 21  1
< [176]  5  9 13 17 21  1  5  9 13 17 21  1  5  9 13 17 21  2  6 10 14 18 22  2  6
< [201] 10 14 18 22  2  6 10 14 18 22  2  6 10 14 18 22  2  6 10 14 18 22  2  6 10
< [226] 14 18 22  2  6 10 14 18 22  2  6 10 14 18 22  2  6 10 14 18 22  2  6 10 14
< [251] 18 22  2  6 10 14 18 22  2  6 10 14 18 22  2  6 10 14 18 22  2  6 10 14 18
< [276] 22  2  6 10 14 18 22  2  6 10 14 18 22  2  6 10 14 18 22  2  6 10 14 18 22
< [301]  2  6 10 14 18 22  2  6 10 14 18 22  2  6 10 14 18 22  2  6 10 14 18 22  2
< [326]  6 10 14 18 22  2  6 10 14 18 22  2  6 10 14 18 22  2  6 10 14 18 22  2  6
< [351] 10 14 18 22  2  6 10 14 18 22  2  6 10 14 18 22  2  6 10 14 18 22  2  6 10
< [376] 14 18 22  2  6 10 14 18 22  3  7 11 15 19 23  3  7 11 15 19 23  3  7 11 15
< [401] 19 23  3  7 11 15 19 23  3  7 11 15 19 23  3  7 11 15 19 23  3  7 11 15 19
< [426] 23  3  7 11 15 19 23  3  7 11 15 19 23  3  7 11 15 19 23  3  7 11 15 19 23
< [451]  3  7 11 15 19 23  3  7 11 15 19 23  3  7 11 15 19 23  3  7 11 15 19 23  3
< [476]  7 11 15 19 23  3  7 11 15 19 23  3  7 11 15 19 23  3  7 11 15 19 23  3  7
< [501] 11 15 19 23  3  7 11 15 19 23  3  7 11 15 19 23  3  7 11 15 19 23  3  7 11
< [526] 15 19 23  3  7 11 15 19 23  3  7 11 15 19 23  3  7 11 15 19 23  3  7 11 15
< [551] 19 23  3  7 11 15 19 23  3  7 11 15 19 23  3  7 11 15 19 23  3  7 11 15 19
< [576] 23  4  8 12 16 20 24  4  8 12 16 20 24  4  8 12 16 20 24  4  8 12 16 20 24
< [601]  4  8 12 16 20 24  4  8 12 16 20 24  4  8 12 16 20 24  4  8 12 16 20 24  4
< [626]  8 12 16 20 24  4  8 12 16 20 24  4  8 12 16 20 24  4  8 12 16 20 24  4  8
< [651] 12 16 20 24  4  8 12 16 20 24  4  8 12 16 20 24  4  8 12 16 20 24  4  8 12
< [676] 16 20 24  4  8 12 16 20 24  4  8 12 16 20 24  4  8 12 16 20 24  4  8 12 16
< [701] 20 24  4  8 12 16 20 24  4  8 12 16 20 24  4  8 12 16 20 24  4  8 12 16 20
< [726] 24  4  8 12 16 20 24  4  8 12 16 20 24  4  8 12 16 20 24  4  8 12 16 20 24
< [751]  4  8 12 16 20 24  4  8 12 16 20 24  4  8 12 16 20 24
< 
< $plateposition
<   [1] "p1D01" "p1D05" "p1D09" "p1D13" "p1D17" "p1D21" "p1H01" "p1H05" "p1H09"
<  [10] "p1H13" "p1H17" "p1H21" "p1L01" "p1L05" "p1L09" "p1L13" "p1L17" "p1L21"
<  [19] "p1P01" "p1P05" "p1P09" "p1P13" "p1P17" "p1P21" "p2D01" "p2D05" "p2D09"
<  [28] "p2D13" "p2D17" "p2D21" "p2H01" "p2H05" "p2H09" "p2H13" "p2H17" "p2H21"
<  [37] "p2L01" "p2L05" "p2L09" "p2L13" "p2L17" "p2L21" "p2P01" "p2P05" "p2P09"
<  [46] "p2P13" "p2P17" "p2P21" "p1C01" "p1C05" "p1C09" "p1C13" "p1C17" "p1C21"
<  [55] "p1G01" "p1G05" "p1G09" "p1G13" "p1G17" "p1G21" "p1K01" "p1K05" "p1K09"
<  [64] "p1K13" "p1K17" "p1K21" "p1O01" "p1O05" "p1O09" "p1O13" "p1O17" "p1O21"
<  [73] "p2C01" "p2C05" "p2C09" "p2C13" "p2C17" "p2C21" "p2G01" "p2G05" "p2G09"
<  [82] "p2G13" "p2G17" "p2G21" "p2K01" "p2K05" "p2K09" "p2K13" "p2K17" "p2K21"
<  [91] "p2O01" "p2O05" "p2O09" "p2O13" "p2O17" "p2O21" "p1B01" "p1B05" "p1B09"
< [100] "p1B13" "p1B17" "p1B21" "p1F01" "p1F05" "p1F09" "p1F13" "p1F17" "p1F21"
< [109] "p1J01" "p1J05" "p1J09" "p1J13" "p1J17" "p1J21" "p1N01" "p1N05" "p1N09"
< [118] "p1N13" "p1N17" "p1N21" "p2B01" "p2B05" "p2B09" "p2B13" "p2B17" "p2B21"
< [127] "p2F01" "p2F05" "p2F09" "p2F13" "p2F17" "p2F21" "p2J01" "p2J05" "p2J09"
< [136] "p2J13" "p2J17" "p2J21" "p2N01" "p2N05" "p2N09" "p2N13" "p2N17" "p2N21"
< [145] "p1A01" "p1A05" "p1A09" "p1A13" "p1A17" "p1A21" "p1E01" "p1E05" "p1E09"
< [154] "p1E13" "p1E17" "p1E21" "p1I01" "p1I05" "p1I09" "p1I13" "p1I17" "p1I21"
< [163] "p1M01" "p1M05" "p1M09" "p1M13" "p1M17" "p1M21" "p2A01" "p2A05" "p2A09"
< [172] "p2A13" "p2A17" "p2A21" "p2E01" "p2E05" "p2E09" "p2E13" "p2E17" "p2E21"
< [181] "p2I01" "p2I05" "p2I09" "p2I13" "p2I17" "p2I21" "p2M01" "p2M05" "p2M09"
< [190] "p2M13" "p2M17" "p2M21" "p1D02" "p1D06" "p1D10" "p1D14" "p1D18" "p1D22"
< [199] "p1H02" "p1H06" "p1H10" "p1H14" "p1H18" "p1H22" "p1L02" "p1L06" "p1L10"
< [208] "p1L14" "p1L18" "p1L22" "p1P02" "p1P06" "p1P10" "p1P14" "p1P18" "p1P22"
< [217] "p2D02" "p2D06" "p2D10" "p2D14" "p2D18" "p2D22" "p2H02" "p2H06" "p2H10"
< [226] "p2H14" "p2H18" "p2H22" "p2L02" "p2L06" "p2L10" "p2L14" "p2L18" "p2L22"
< [235] "p2P02" "p2P06" "p2P10" "p2P14" "p2P18" "p2P22" "p1C02" "p1C06" "p1C10"
< [244] "p1C14" "p1C18" "p1C22" "p1G02" "p1G06" "p1G10" "p1G14" "p1G18" "p1G22"
< [253] "p1K02" "p1K06" "p1K10" "p1K14" "p1K18" "p1K22" "p1O02" "p1O06" "p1O10"
< [262] "p1O14" "p1O18" "p1O22" "p2C02" "p2C06" "p2C10" "p2C14" "p2C18" "p2C22"
< [271] "p2G02" "p2G06" "p2G10" "p2G14" "p2G18" "p2G22" "p2K02" "p2K06" "p2K10"
< [280] "p2K14" "p2K18" "p2K22" "p2O02" "p2O06" "p2O10" "p2O14" "p2O18" "p2O22"
< [289] "p1B02" "p1B06" "p1B10" "p1B14" "p1B18" "p1B22" "p1F02" "p1F06" "p1F10"
< [298] "p1F14" "p1F18" "p1F22" "p1J02" "p1J06" "p1J10" "p1J14" "p1J18" "p1J22"
< [307] "p1N02" "p1N06" "p1N10" "p1N14" "p1N18" "p1N22" "p2B02" "p2B06" "p2B10"
< [316] "p2B14" "p2B18" "p2B22" "p2F02" "p2F06" "p2F10" "p2F14" "p2F18" "p2F22"
< [325] "p2J02" "p2J06" "p2J10" "p2J14" "p2J18" "p2J22" "p2N02" "p2N06" "p2N10"
< [334] "p2N14" "p2N18" "p2N22" "p1A02" "p1A06" "p1A10" "p1A14" "p1A18" "p1A22"
< [343] "p1E02" "p1E06" "p1E10" "p1E14" "p1E18" "p1E22" "p1I02" "p1I06" "p1I10"
< [352] "p1I14" "p1I18" "p1I22" "p1M02" "p1M06" "p1M10" "p1M14" "p1M18" "p1M22"
< [361] "p2A02" "p2A06" "p2A10" "p2A14" "p2A18" "p2A22" "p2E02" "p2E06" "p2E10"
< [370] "p2E14" "p2E18" "p2E22" "p2I02" "p2I06" "p2I10" "p2I14" "p2I18" "p2I22"
< [379] "p2M02" "p2M06" "p2M10" "p2M14" "p2M18" "p2M22" "p1D03" "p1D07" "p1D11"
< [388] "p1D15" "p1D19" "p1D23" "p1H03" "p1H07" "p1H11" "p1H15" "p1H19" "p1H23"
< [397] "p1L03" "p1L07" "p1L11" "p1L15" "p1L19" "p1L23" "p1P03" "p1P07" "p1P11"
< [406] "p1P15" "p1P19" "p1P23" "p2D03" "p2D07" "p2D11" "p2D15" "p2D19" "p2D23"
< [415] "p2H03" "p2H07" "p2H11" "p2H15" "p2H19" "p2H23" "p2L03" "p2L07" "p2L11"
< [424] "p2L15" "p2L19" "p2L23" "p2P03" "p2P07" "p2P11" "p2P15" "p2P19" "p2P23"
< [433] "p1C03" "p1C07" "p1C11" "p1C15" "p1C19" "p1C23" "p1G03" "p1G07" "p1G11"
< [442] "p1G15" "p1G19" "p1G23" "p1K03" "p1K07" "p1K11" "p1K15" "p1K19" "p1K23"
< [451] "p1O03" "p1O07" "p1O11" "p1O15" "p1O19" "p1O23" "p2C03" "p2C07" "p2C11"
< [460] "p2C15" "p2C19" "p2C23" "p2G03" "p2G07" "p2G11" "p2G15" "p2G19" "p2G23"
< [469] "p2K03" "p2K07" "p2K11" "p2K15" "p2K19" "p2K23" "p2O03" "p2O07" "p2O11"
< [478] "p2O15" "p2O19" "p2O23" "p1B03" "p1B07" "p1B11" "p1B15" "p1B19" "p1B23"
< [487] "p1F03" "p1F07" "p1F11" "p1F15" "p1F19" "p1F23" "p1J03" "p1J07" "p1J11"
< [496] "p1J15" "p1J19" "p1J23" "p1N03" "p1N07" "p1N11" "p1N15" "p1N19" "p1N23"
< [505] "p2B03" "p2B07" "p2B11" "p2B15" "p2B19" "p2B23" "p2F03" "p2F07" "p2F11"
< [514] "p2F15" "p2F19" "p2F23" "p2J03" "p2J07" "p2J11" "p2J15" "p2J19" "p2J23"
< [523] "p2N03" "p2N07" "p2N11" "p2N15" "p2N19" "p2N23" "p1A03" "p1A07" "p1A11"
< [532] "p1A15" "p1A19" "p1A23" "p1E03" "p1E07" "p1E11" "p1E15" "p1E19" "p1E23"
< [541] "p1I03" "p1I07" "p1I11" "p1I15" "p1I19" "p1I23" "p1M03" "p1M07" "p1M11"
< [550] "p1M15" "p1M19" "p1M23" "p2A03" "p2A07" "p2A11" "p2A15" "p2A19" "p2A23"
< [559] "p2E03" "p2E07" "p2E11" "p2E15" "p2E19" "p2E23" "p2I03" "p2I07" "p2I11"
< [568] "p2I15" "p2I19" "p2I23" "p2M03" "p2M07" "p2M11" "p2M15" "p2M19" "p2M23"
< [577] "p1D04" "p1D08" "p1D12" "p1D16" "p1D20" "p1D24" "p1H04" "p1H08" "p1H12"
< [586] "p1H16" "p1H20" "p1H24" "p1L04" "p1L08" "p1L12" "p1L16" "p1L20" "p1L24"
< [595] "p1P04" "p1P08" "p1P12" "p1P16" "p1P20" "p1P24" "p2D04" "p2D08" "p2D12"
< [604] "p2D16" "p2D20" "p2D24" "p2H04" "p2H08" "p2H12" "p2H16" "p2H20" "p2H24"
< [613] "p2L04" "p2L08" "p2L12" "p2L16" "p2L20" "p2L24" "p2P04" "p2P08" "p2P12"
< [622] "p2P16" "p2P20" "p2P24" "p1C04" "p1C08" "p1C12" "p1C16" "p1C20" "p1C24"
< [631] "p1G04" "p1G08" "p1G12" "p1G16" "p1G20" "p1G24" "p1K04" "p1K08" "p1K12"
< [640] "p1K16" "p1K20" "p1K24" "p1O04" "p1O08" "p1O12" "p1O16" "p1O20" "p1O24"
< [649] "p2C04" "p2C08" "p2C12" "p2C16" "p2C20" "p2C24" "p2G04" "p2G08" "p2G12"
< [658] "p2G16" "p2G20" "p2G24" "p2K04" "p2K08" "p2K12" "p2K16" "p2K20" "p2K24"
< [667] "p2O04" "p2O08" "p2O12" "p2O16" "p2O20" "p2O24" "p1B04" "p1B08" "p1B12"
< [676] "p1B16" "p1B20" "p1B24" "p1F04" "p1F08" "p1F12" "p1F16" "p1F20" "p1F24"
< [685] "p1J04" "p1J08" "p1J12" "p1J16" "p1J20" "p1J24" "p1N04" "p1N08" "p1N12"
< [694] "p1N16" "p1N20" "p1N24" "p2B04" "p2B08" "p2B12" "p2B16" "p2B20" "p2B24"
< [703] "p2F04" "p2F08" "p2F12" "p2F16" "p2F20" "p2F24" "p2J04" "p2J08" "p2J12"
< [712] "p2J16" "p2J20" "p2J24" "p2N04" "p2N08" "p2N12" "p2N16" "p2N20" "p2N24"
< [721] "p1A04" "p1A08" "p1A12" "p1A16" "p1A20" "p1A24" "p1E04" "p1E08" "p1E12"
< [730] "p1E16" "p1E20" "p1E24" "p1I04" "p1I08" "p1I12" "p1I16" "p1I20" "p1I24"
< [739] "p1M04" "p1M08" "p1M12" "p1M16" "p1M20" "p1M24" "p2A04" "p2A08" "p2A12"
< [748] "p2A16" "p2A20" "p2A24" "p2E04" "p2E08" "p2E12" "p2E16" "p2E20" "p2E24"
< [757] "p2I04" "p2I08" "p2I12" "p2I16" "p2I20" "p2I24" "p2M04" "p2M08" "p2M12"
< [766] "p2M16" "p2M20" "p2M24"
< 
< > 
< > ### merge.rglist
< > 
< > R <- G <- matrix(11:14,4,2)
< > rownames(R) <- rownames(G) <- c("a","a","b","c")
< > RG1 <- new("RGList",list(R=R,G=G))
< > R <- G <- matrix(21:24,4,2)
< > rownames(R) <- rownames(G) <- c("b","a","a","c")
< > RG2 <- new("RGList",list(R=R,G=G))
< > merge(RG1,RG2)
< An object of class "RGList"
< $R
<   [,1] [,2] [,3] [,4]
< a   11   11   22   22
< a   12   12   23   23
< b   13   13   21   21
< c   14   14   24   24
< 
< $G
<   [,1] [,2] [,3] [,4]
< a   11   11   22   22
< a   12   12   23   23
< b   13   13   21   21
< c   14   14   24   24
< 
< > merge(RG2,RG1)
< An object of class "RGList"
< $R
<   [,1] [,2] [,3] [,4]
< b   21   21   13   13
< a   22   22   11   11
< a   23   23   12   12
< c   24   24   14   14
< 
< $G
<   [,1] [,2] [,3] [,4]
< b   21   21   13   13
< a   22   22   11   11
< a   23   23   12   12
< c   24   24   14   14
< 
< > 
< > ### background correction
< > RG <- new("RGList", list(R=c(1,2,3,4),G=c(1,2,3,4),Rb=c(2,2,2,2),Gb=c(2,2,2,2)))
< > backgroundCorrect(RG)
< An object of class "RGList"
< $R
< [1] -1  0  1  2
< 
< $G
< [1] -1  0  1  2
< 
< > backgroundCorrect(RG, method="half")
< An object of class "RGList"
< $R
< [1] 0.5 0.5 1.0 2.0
< 
< $G
< [1] 0.5 0.5 1.0 2.0
< 
< > backgroundCorrect(RG, method="minimum")
< An object of class "RGList"
< $R
<      [,1]
< [1,]  0.5
< [2,]  0.5
< [3,]  1.0
< [4,]  2.0
< 
< $G
<      [,1]
< [1,]  0.5
< [2,]  0.5
< [3,]  1.0
< [4,]  2.0
< 
< > backgroundCorrect(RG, offset=5)
< An object of class "RGList"
< $R
< [1] 4 5 6 7
< 
< $G
< [1] 4 5 6 7
< 
< > 
< > ### normalizeWithinArrays
< > 
< > library(sma)
< > data(MouseArray)
< Warning message:
< file 'MouseArray.RData' has magic number 'RDX1'
<    Use of save versions prior to 2 is deprecated 
< > MA <- normalizeWithinArrays(mouse.data, mouse.setup, method="robustspline")
< > MA$M[1:5,]
<             [,1]        [,2]        [,3]        [,4]       [,5]        [,6]
< [1,] -0.21539109 -0.79670669 -0.55011008  0.14243756 -0.3933328  0.86741957
< [2,]  0.06449435  0.16873653  0.26020426  0.92440874  0.6640048  1.30672583
< [3,] -0.23149571 -0.66662065 -0.68092134 -0.09651125 -0.4205728 -0.31124721
< [4,] -0.20090146 -0.09709476 -0.28354313  0.32830186  0.1916112 -0.09738907
< [5,] -0.86822005 -0.13192148 -0.08634807 -0.01017014  0.2763200 -0.22570480
< > MA <- normalizeWithinArrays(mouse.data, mouse.setup)
< > MA$M[1:5,]
<             [,1]        [,2]        [,3]        [,4]       [,5]       [,6]
< [1,] -0.22006681 -0.85229101 -0.61528102  0.07080387 -0.4017245  0.8790516
< [2,]  0.06720908  0.11711457  0.21083609  0.99616190  0.6494259  1.3351120
< [3,] -0.23069447 -0.71229077 -0.72631373 -0.12375213 -0.4262350 -0.3237170
< [4,] -0.17262990 -0.06186499 -0.28347377  0.27201473  0.2028371 -0.1018497
< [5,] -0.83900000 -0.09643457 -0.08877846 -0.06550247  0.2807478 -0.2229941
< > 
< > ### normalizeBetweenArrays
< > 
< > MA <- normalizeBetweenArrays(MA,method="scale")
< > MA$M[1:5,]
<             [,1]        [,2]       [,3]        [,4]       [,5]       [,6]
< [1,] -0.22060913 -0.97047013 -0.7132995  0.05299212 -0.4035381  0.8835727
< [2,]  0.06737471  0.13335374  0.2444237  0.74556284  0.6523577  1.3419787
< [3,] -0.23126298 -0.81105738 -0.8420205 -0.09262048 -0.4281592 -0.3253819
< [4,] -0.17305532 -0.07044322 -0.3286331  0.20358545  0.2037528 -0.1023735
< [5,] -0.84106756 -0.10980624 -0.1029215 -0.04902437  0.2820152 -0.2241410
< > MA$A[1:5,]
<           [,1]      [,2]      [,3]      [,4]      [,5]      [,6]
< [1,] 11.332980 11.198841 11.337353  9.693899 11.196822 10.506374
< [2,] 11.245664 11.074098 11.051345 10.931562 11.273305 10.008818
< [3,] 10.113995 10.923628 12.322088  9.875351 11.096463 10.829522
< [4,]  8.390963  9.019036  8.720987  9.774672  8.826249  9.113240
< [5,]  8.684837  9.017042  8.406961  9.477079  8.739632  8.557627
< > MA <- normalizeBetweenArrays(MA,method="quantile")
< > MA$M[1:5,]
<             [,1]       [,2]       [,3]        [,4]       [,5]       [,6]
< [1,] -0.31703694 -0.9938725 -0.5791881  0.03617137 -0.3769488  0.9820991
< [2,]  0.03923233  0.1066559  0.2312904  0.76612052  0.6368203  1.4728996
< [3,] -0.27566044 -0.8580353 -0.7504079 -0.08854074 -0.4200884 -0.2960210
< [4,] -0.11946685 -0.1095793 -0.2985336  0.15876207  0.2612499 -0.1006169
< [5,] -0.67628732 -0.1634459 -0.0938785 -0.05338925  0.3477450 -0.2227479
< > MA$A[1:5,]
<           [,1]      [,2]      [,3]      [,4]      [,5]     [,6]
< [1,] 11.478807 11.311915 11.142829  9.749722 11.137385 10.56415
< [2,] 11.369349 11.191410 10.896307 10.893490 11.205219 10.04138
< [3,] 10.124225 11.010219 12.026393  9.906701 11.045121 10.91363
< [4,]  8.521087  8.771148  8.810923  9.817860  8.681051  9.06633
< [5,]  8.772261  8.766051  8.538890  9.580934  8.567045  8.55471
< > 
< > ### unwrapdups
< > 
< > M <- matrix(1:12,6,2)
< > unwrapdups(M,ndups=1)
<      [,1] [,2]
< [1,]    1    7
< [2,]    2    8
< [3,]    3    9
< [4,]    4   10
< [5,]    5   11
< [6,]    6   12
< > unwrapdups(M,ndups=2)
<      [,1] [,2] [,3] [,4]
< [1,]    1    2    7    8
< [2,]    3    4    9   10
< [3,]    5    6   11   12
< > unwrapdups(M,ndups=3)
<      [,1] [,2] [,3] [,4] [,5] [,6]
< [1,]    1    2    3    7    8    9
< [2,]    4    5    6   10   11   12
< > unwrapdups(M,ndups=2,spacing=3)
<      [,1] [,2] [,3] [,4]
< [1,]    1    4    7   10
< [2,]    2    5    8   11
< [3,]    3    6    9   12
< > 
< > ### trigammaInverse
< > 
< > trigammaInverse(c(1e-6,NA,5,1e6))
< [1] 1.000000e+06           NA 4.961687e-01 1.000001e-03
< > 
< > ### lm.series, contrasts.fit, ebayes
< > 
< > M <- matrix(rnorm(10*6,sd=0.3),10,6)
< > M[1,1:3] <- M[1,1:3] + 2
< > design <- cbind(First3Arrays=c(1,1,1,0,0,0),Last3Arrays=c(0,0,0,1,1,1))
< > fit <- lm.series(M,design=design)
< > contrast.matrix <- cbind(First3=c(1,0),Last3=c(0,1),"Last3-First3"=c(-1,1))
< > fit2 <- contrasts.fit(fit,contrasts=contrast.matrix)
< > eb <- ebayes(fit2)
< > 
< > eb$t
<            First3      Last3 Last3-First3
<  [1,] 13.01360810  0.8094614  -8.62963489
<  [2,] -0.08220793 -0.2496031  -0.11836624
<  [3,]  0.53689924  0.1037124  -0.30630936
<  [4,] -0.64950290 -0.6643004  -0.01046340
<  [5,] -0.12967606 -0.6044961  -0.33574846
<  [6,]  1.00443329  0.1749033  -0.58656627
<  [7,] -0.41799559 -0.3567558   0.04330306
<  [8,]  0.04763415  1.7686344   1.21693097
<  [9,] -1.82026162  0.6205108   1.72588671
< [10,] -1.66163020  2.0938216   2.65550546
< > eb$s2.prior
< [1] 0.07549435
< > eb$s2.post
<  [1] 0.07549435 0.07549435 0.07549435 0.07549435 0.07549435 0.07549435
<  [7] 0.07549435 0.07549435 0.07549435 0.07549435
< > eb$df.prior
< [1] Inf
< > eb$lods
<          First3     Last3 Last3-First3
<  [1,] 76.894615 -4.836703    29.863710
<  [2,] -7.551544 -5.007910    -7.137158
<  [3,] -7.411171 -5.022793    -7.097495
<  [4,] -7.344554 -4.898476    -7.144066
<  [5,] -7.546529 -4.920386    -7.088102
<  [6,] -7.051826 -5.017066    -6.973142
<  [7,] -7.467789 -4.989149    -7.143189
<  [8,] -7.553783 -4.122674    -6.408184
<  [9,] -5.902688 -4.914721    -5.663877
< [10,] -6.178115 -3.760000    -3.639805
< > eb$p.value
<             First3      Last3 Last3-First3
<  [1,] 1.023910e-38 0.41824980 6.154813e-18
<  [2,] 9.344814e-01 0.80289433 9.057775e-01
<  [3,] 5.913372e-01 0.91739759 7.593691e-01
<  [4,] 5.160134e-01 0.50649808 9.916516e-01
<  [5,] 8.968227e-01 0.54551387 7.370606e-01
<  [6,] 3.151698e-01 0.86115561 5.574950e-01
<  [7,] 6.759503e-01 0.72127462 9.654600e-01
<  [8,] 9.620078e-01 0.07695490 2.236305e-01
<  [9,] 6.871917e-02 0.53492156 8.436780e-02
< [10,] 9.658694e-02 0.03627587 7.918965e-03
< > eb$var.prior
< [1] 123.7528665   0.4556155 108.4630118
< > 
< > ### toptable
< > 
< > toptable(fit)
<               M           t      P.Value    adj.P.Val         B
< 1   2.064402265 13.01360810 1.023910e-38 1.023910e-37 76.894615
< 9  -0.288755599 -1.82026162 6.871917e-02 3.219565e-01 -5.902688
< 10 -0.263591244 -1.66163020 9.658694e-02 3.219565e-01 -6.178115
< 6   0.159337391  1.00443329 3.151698e-01 7.879245e-01 -7.051826
< 4  -0.103033320 -0.64950290 5.160134e-01 9.620078e-01 -7.344554
< 3   0.085170539  0.53689924 5.913372e-01 9.620078e-01 -7.411171
< 7  -0.066308362 -0.41799559 6.759503e-01 9.620078e-01 -7.467789
< 5  -0.020571048 -0.12967606 8.968227e-01 9.620078e-01 -7.546529
< 2  -0.013040982 -0.08220793 9.344814e-01 9.620078e-01 -7.551544
< 8   0.007556402  0.04763415 9.620078e-01 9.620078e-01 -7.553783
< > 
< > ### duplicateCorrelation
< > 
< > cor.out <- duplicateCorrelation(M)
< 
< Attaching package: 'statmod'
< 
< 
< 	The following object(s) are masked from package:limma :
< 
< 	 matvec 
< 
< 	The following object(s) are masked from package:limma :
< 
< 	 vecmat 
< 
< > cor.out$consensus.correlation
< [1] -0.1300222
< > cor.out$atanh.correlations
< [1] -0.3496702 -0.3528761  0.1320187 -0.7957172  0.7124326
< > 
< > ### gls.series
< > 
< > fit <- gls.series(M,design,correlation=cor.out$cor)
< > fit$coefficients
<      First3Arrays Last3Arrays
< [1,]   1.02568064  0.04440632
< [2,]  -0.00893139 -0.04446419
< [3,]   0.06938317 -0.03407404
< [4,]  -0.02937598  0.11198606
< [5,]  -0.27617342  0.21529287
< > fit$stdev.unscaled
<      First3Arrays Last3Arrays
< [1,]    0.3807838   0.3807838
< [2,]    0.3807838   0.3807838
< [3,]    0.3807838   0.3807838
< [4,]    0.3807838   0.3807838
< [5,]    0.3807838   0.3807838
< > fit$sigma
< [1] 0.7880432 0.2880540 0.1997484 0.2750895 0.2621346
< > fit$df.residual
< [1] 10 10 10 10 10
< > 
< > ### mrlm
< > 
< > fit <- mrlm(M,design)
< > fit$coef
<       First3Arrays Last3Arrays
<  [1,]  2.064402265  0.23453509
<  [2,] -0.013040982 -0.15267834
<  [3,] -0.030835828  0.01645232
<  [4,] -0.103033320 -0.10538070
<  [5,] -0.020571048 -0.09589370
<  [6,]  0.159337391  0.02774563
<  [7,] -0.066308362 -0.05659364
<  [8,]  0.007556402  0.38166839
<  [9,] -0.288755599  0.09843418
< [10,] -0.263591244  0.33215155
< > fit$stdev.unscaled
<       First3Arrays Last3Arrays
<  [1,]    0.5773503   0.7315593
<  [2,]    0.5773503   0.6511403
<  [3,]    0.6269590   0.5773503
<  [4,]    0.5773503   0.5773503
<  [5,]    0.5773503   0.5773503
<  [6,]    0.5773503   0.5773503
<  [7,]    0.5773503   0.5773503
<  [8,]    0.5773503   0.6527609
<  [9,]    0.5773503   0.5773503
< [10,]    0.5773503   0.5773503
< > fit$sigma
<  [1] 0.0755165 0.1410025 0.3087025 0.1390960 0.3289335 0.1719261 0.4295126
<  [8] 0.1197697 0.3906706 0.2267115
< > fit$df.residual
<  [1] 4 4 4 4 4 4 4 4 4 4
< > 
< > # Similar to Mette Langaas 19 May 2004
< > set.seed(123)
< > narrays <- 9
< > ngenes <- 5
< > mu <- 0
< > alpha <- 2
< > beta <- -2
< > epsilon <- matrix(rnorm(narrays*ngenes,0,1),ncol=narrays)
< > X <- cbind(rep(1,9),c(0,0,0,1,1,1,0,0,0),c(0,0,0,0,0,0,1,1,1))
< > dimnames(X) <- list(1:9,c("mu","alpha","beta"))
< > yvec <- mu*X[,1]+alpha*X[,2]+beta*X[,3]
< > ymat <- matrix(rep(yvec,ngenes),ncol=narrays,byrow=T)+epsilon
< > ymat[5,1:2] <- NA
< > fit <- lmFit(ymat,design=X)
< > test.contr <- cbind(c(0,1,-1),c(1,1,0),c(1,0,1))
< > dimnames(test.contr) <- list(1:3,c("alpha-beta","mu+alpha","mu+beta"))
< > fit2 <- contrasts.fit(fit,contrasts=test.contr)
< > eBayes(fit2)
< An object of class "MArrayLM"
< $coefficients
<      alpha-beta mu+alpha   mu+beta
< [1,]   3.537333 1.677465 -1.859868
< [2,]   4.355578 2.372554 -1.983024
< [3,]   3.197645 1.053584 -2.144061
< [4,]   2.697734 1.611443 -1.086291
< [5,]   3.502304 2.051995 -1.450309
< 
< $stdev.unscaled
<      alpha-beta  mu+alpha   mu+beta
< [1,]  0.8164966 0.5773503 0.5773503
< [2,]  0.8164966 0.5773503 0.5773503
< [3,]  0.8164966 0.5773503 0.5773503
< [4,]  0.8164966 0.5773503 0.5773503
< [5,]  1.1547005 0.8368633 0.8368633
< 
< $sigma
< [1] 1.3425032 0.4647155 1.1993444 0.9428569 0.9421509
< 
< $df.residual
< [1] 6 6 6 6 4
< 
< $cov.coefficients
<            alpha-beta      mu+alpha       mu+beta
< alpha-beta  0.6666667  3.333333e-01 -3.333333e-01
< mu+alpha    0.3333333  3.333333e-01 -1.821460e-17
< mu+beta    -0.3333333 -1.821460e-17  3.333333e-01
< 
< $method
< [1] "ls"
< 
< $design
<   mu alpha beta
< 1  1     0    0
< 2  1     0    0
< 3  1     0    0
< 4  1     1    0
< 5  1     1    0
< 6  1     1    0
< 7  1     0    1
< 8  1     0    1
< 9  1     0    1
< 
< $Amean
< [1]  0.2034961  0.1954604 -0.2863347  0.1188659  0.1784593
< 
< $contrasts
<   alpha-beta mu+alpha mu+beta
< 1          0        1       1
< 2          1        1       0
< 3         -1        0       1
< 
< $df.prior
< [1] 9.306153
< 
< $s2.prior
< [1] 0.923179
< 
< $var.prior
< [1] 17.33142 17.33142 12.26855
< 
< $proportion
< [1] 0.01
< 
< $s2.post
< [1] 1.2677996 0.6459499 1.1251558 0.9097727 0.9124980
< 
< $t
<      alpha-beta mu+alpha   mu+beta
< [1,]   3.847656 2.580411 -2.860996
< [2,]   6.637308 5.113018 -4.273553
< [3,]   3.692066 1.720376 -3.500994
< [4,]   3.464003 2.926234 -1.972606
< [5,]   3.175181 2.566881 -1.814221
< 
< $p.value
<        alpha-beta     mu+alpha      mu+beta
< [1,] 1.529450e-03 0.0206493481 0.0117123495
< [2,] 7.144893e-06 0.0001195844 0.0006385076
< [3,] 2.109270e-03 0.1055117477 0.0031325769
< [4,] 3.381970e-03 0.0102514264 0.0668844448
< [5,] 7.124839e-03 0.0230888584 0.0922478630
< 
< $lods
<      alpha-beta  mu+alpha    mu+beta
< [1,]  -1.013417 -3.702133 -3.0332393
< [2,]   3.981496  1.283349 -0.2615911
< [3,]  -1.315036 -5.168621 -1.7864101
< [4,]  -1.757103 -3.043209 -4.6191869
< [5,]  -2.257358 -3.478267 -4.5683738
< 
< $F
< [1]  7.421911 22.203107  7.608327  6.227010  5.060579
< 
< $F.p.value
< [1] 5.581800e-03 2.988923e-05 5.080726e-03 1.050148e-02 2.320274e-02
< 
< > 
< > ### uniquegenelist
< > 
< > uniquegenelist(letters[1:8],ndups=2)
< [1] "a" "c" "e" "g"
< > uniquegenelist(letters[1:8],ndups=2,spacing=2)
< [1] "a" "b" "e" "f"
< > 
< > ### classifyTests
< > 
< > tstat <- matrix(c(0,5,0, 0,2.5,0, -2,-2,2, 1,1,1), 4, 3, byrow=TRUE)
< > classifyTestsF(tstat)
< TestResults matrix
<      [,1] [,2] [,3]
< [1,]    0    1    0
< [2,]    0    0    0
< [3,]   -1   -1    1
< [4,]    0    0    0
< > FStat(tstat)
< [1] 8.333333 2.083333 4.000000 1.000000
< attr(,"df1")
< [1] 3
< attr(,"df2")
< [1] Inf
< > classifyTestsT(tstat)
< TestResults matrix
<      [,1] [,2] [,3]
< [1,]    0    1    0
< [2,]    0    0    0
< [3,]    0    0    0
< [4,]    0    0    0
< > classifyTestsP(tstat)
< TestResults matrix
<      [,1] [,2] [,3]
< [1,]    0    1    0
< [2,]    0    1    0
< [3,]    0    0    0
< [4,]    0    0    0
< > 
 OK
make[1]: Leaving directory `/extra/loc/biocbuild/1.9d/Rpacks/limma.Rcheck/tests'
 OK
* checking package vignettes in 'inst/doc' ... OK
* creating limma-manual.tex ... OK
* checking limma-manual.tex ... OK

limma.Rcheck/00install.out:

* Installing *source* package 'limma' ...
** R
** inst
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'limma'
     Formats: text html latex example 
  01Introduction                    text    html    latex
  02classes                         text    html    latex
  03reading                         text    html    latex
  04Background                      text    html    latex
  05Normalization                   text    html    latex
  06linearmodels                    text    html    latex
  07SingleChannel                   text    html    latex
  08Tests                           text    html    latex
  09Diagnostics                     text    html    latex
  10Other                           text    html    latex
  LargeDataObject                   text    html    latex   example
  PrintLayout                       text    html    latex   example
  TestResults                       text    html    latex   example
  anova-method                      text    html    latex
  arrayWeights                      text    html    latex   example
  arrayWeightsQuick                 text    html    latex   example
  asMatrixWeights                   text    html    latex   example
  asdataframe                       text    html    latex
  asmalist                          text    html    latex
  asmatrix                          text    html    latex
  auROC                             text    html    latex   example
  avedups                           text    html    latex
  backgroundcorrect                 text    html    latex   example
  blockDiag                         text    html    latex   example
  bwss                              text    html    latex
  bwss.matrix                       text    html    latex
  cbind                             text    html    latex   example
  changelog                         text    html    latex
  channel2M                         text    html    latex   example
  classifytests                     text    html    latex   example
  contrasts.fit                     text    html    latex   example
  controlStatus                     text    html    latex   example
  convest                           text    html    latex   example
  decideTests                       text    html    latex
  dim                               text    html    latex   example
  dimnames                          text    html    latex
  dnormexp                          text    html    latex
  dupcor                            text    html    latex   example
  ebayes                            text    html    latex   example
  exprsMA                           text    html    latex
  exprset2                          text    html    latex
  fitfdist                          text    html    latex
  fitted.MArrayLM                   text    html    latex
  geneSetTest                       text    html    latex   example
  getColClasses                     text    html    latex   example
  getSpacing                        text    html    latex   example
  getlayout                         text    html    latex   example
  gls.series                        text    html    latex
  gridspotrc                        text    html    latex
  heatdiagram                       text    html    latex   example
  helpMethods                       text    html    latex   example
  imageplot                         text    html    latex   example
  imageplot3by2                     text    html    latex
  intraspotCorrelation              text    html    latex   example
  isfullrank                        text    html    latex   example
  isnumeric                         text    html    latex   example
  kooperberg                        text    html    latex   example
  limmaUsersGuide                   text    html    latex   example
  lm.series                         text    html    latex
  lmFit                             text    html    latex   example
  lmscFit                           text    html    latex   example
  loessfit                          text    html    latex   example
  m.spot                            text    html    latex
  ma3x3                             text    html    latex   example
  makeContrasts                     text    html    latex   example
  makeunique                        text    html    latex   example
  malist                            text    html    latex
  marraylm                          text    html    latex
  matvec                            text    html    latex   example
  mdplot                            text    html    latex
  merge                             text    html    latex   example
  modelMatrix                       text    html    latex   example
  modifyWeights                     text    html    latex   example
  mrlm                              text    html    latex
  normalizeMedianAbsValues          text    html    latex   example
  normalizeRobustSpline             text    html    latex   example
  normalizeWithinArrays             text    html    latex   example
  normalizebetweenarrays            text    html    latex   example
  normalizeprintorder               text    html    latex   example
  normalizequantiles                text    html    latex
  normexp                           text    html    latex
  normexpfit                        text    html    latex   example
  normexpsignal                     text    html    latex   example
  plotDensities                     text    html    latex   example
  plotFB                            text    html    latex
  plotlines                         text    html    latex
  plotma                            text    html    latex   example
  plotma3by2                        text    html    latex
  plotprinttiploess                 text    html    latex
  poolvar                           text    html    latex   example
  printHead                         text    html    latex
  printorder                        text    html    latex   example
  protectMetachar                   text    html    latex   example
  qqt                               text    html    latex   example
  qualwt                            text    html    latex   example
  read.maimages                     text    html    latex   example
  read.matrix                       text    html    latex
  read.series                       text    html    latex
  readGPRHeader                     text    html    latex
  readImaGeneHeader                 text    html    latex   example
  readSpotTypes                     text    html    latex
  readTargets                       text    html    latex
  readgal                           text    html    latex   example
  removeext                         text    html    latex   example
  residuals.MArrayLM                text    html    latex
  rg.genepix                        text    html    latex
  rg.quantarray                     text    html    latex
  rg.series.spot                    text    html    latex
  rg.spot                           text    html    latex
  rglist                            text    html    latex
  splitName                         text    html    latex   example
  squeezeVar                        text    html    latex   example
  subsetting                        text    html    latex   example
  summary                           text    html    latex
  targetsA2C                        text    html    latex   example
  tmixture                          text    html    latex
  toptable                          text    html    latex   example
  trigammainverse                   text    html    latex   example
  trimWhiteSpace                    text    html    latex   example
  uniquegenelist                    text    html    latex   example
  unwrapdups                        text    html    latex   example
  venn                              text    html    latex   example
  volcanoplot                       text    html    latex   example
  weightedmedian                    text    html    latex   example
  writefit                          text    html    latex
  wtVariables                       text    html    latex   example
  zscore                            text    html    latex   example
** building package indices ...
* DONE (limma)