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* checking for file ‘genefu/DESCRIPTION’ ... OK
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* installing the package to process help pages
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[]\T1/zi4/m/n/9 predout <- claudinLow(x=train$xd, classes=as.matrix(train$clas
ses$Group,ncol=1), y=test$xd)[]
[6] [7]
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[] \T1/zi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
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[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
[12] [13] [14]
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
omics Con-sor-tium us-ing Affymetrix hgu133plus2
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[]\T1/ptm/m/n/10 International Ge-nomics Con-sor-tium, [][]$\T1/zi4/m/n/10 http
: / / www . intgen . org / research-[]services / biobanking-[]experience /
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
11\T1/ptm/m/n/10 (2):R18
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[]\T1/zi4/m/n/10 ihc4(ER, PGR, HER2, Ki67,age,size,grade,node,ana,scoreWithCli
nical=FALSE, na.rm = FALSE)[]
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[]\T1/zi4/m/n/9 ihc4(ER=sample(x=1:10, size=count,replace=TRUE),PGR=sample(x=1
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[]\T1/zi4/m/n/9 age=demo.nkis[,"age"],size=demo.nkis[ ,"size"],grade=demo.nkis
[ ,"grade"],node=demo.nkis[ ,"node"],[]
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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
and probes in columns,
[28]
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[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
named "En-trez-Gene.ID",
[29] [30] [31] [32] [33] [34] [35] [36] [37]
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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/zi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/zi4/m/n/10 do.mapping=TRUE
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[]\T1/zi4/m/n/9 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis,
gmap="entrezgene", do.mapping=TRUE)[]
[40]
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[]\T1/zi4/m/n/9 ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap
="entrezgene", do.mapping=TRUE)[]
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[]\T1/zi4/m/n/10 gmap = c("entrezgene", "ensembl_gene_id", "hgnc_symbol", "uni
gene", "refseq_mrna"),[]
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[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the
gene ex-pres-sions (see [][]\T1/zi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ).
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[]\T1/zi4/m/n/9 tt <- data.frame(matrix(NA, nrow=3, ncol=3, dimnames=list(1:3,
paste("column", 1:3, sep="."))),[]
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[][][]$\T1/zi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][]
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
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[][][]\T1/zi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
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[][][]$\T1/zi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
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[]\T1/zi4/m/n/9 predout <- claudinLow(x=train$xd, classes=as.matrix(train$clas
ses$Group,ncol=1), y=test$xd)[]
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[] \T1/zi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
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[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
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[]\T1/ptm/m/n/10 International Ge-nomics Con-sor-tium, [][]$\T1/zi4/m/n/10 http
: / / www . intgen . org / research-[]services / biobanking-[]experience /
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e-sis, must be one of "two.sided"
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
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[]\T1/zi4/m/n/10 ihc4(ER, PGR, HER2, Ki67,age,size,grade,node,ana,scoreWithCli
nical=FALSE, na.rm = FALSE)[]
[24]
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[]\T1/zi4/m/n/9 ihc4(ER=sample(x=1:10, size=count,replace=TRUE),PGR=sample(x=1
:10, size=count,replace=TRUE),[]
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[]\T1/zi4/m/n/9 age=demo.nkis[,"age"],size=demo.nkis[ ,"size"],grade=demo.nkis
[ ,"grade"],node=demo.nkis[ ,"node"],[]
[25] [26] [27] [28]
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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
and probes in columns,
[29]
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[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
named "En-trez-Gene.ID",
[30] [31] [32] [33] [34] [35] [36] [37] [38]
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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/zi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/zi4/m/n/10 do.mapping=TRUE
[39]
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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/zi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/zi4/m/n/10 do.mapping=TRUE
[40]
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[]\T1/zi4/m/n/9 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis,
gmap="entrezgene", do.mapping=TRUE)[]
[41]
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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/zi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/zi4/m/n/10 do.mapping=TRUE
[42]
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[]\T1/zi4/m/n/9 ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap
="entrezgene", do.mapping=TRUE)[]
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[]\T1/zi4/m/n/10 gmap = c("entrezgene", "ensembl_gene_id", "hgnc_symbol", "uni
gene", "refseq_mrna"),[]
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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/zi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/zi4/m/n/10 do.mapping=TRUE
[43] [44]
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[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the
gene ex-pres-sions (see [][]\T1/zi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ).
[45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55]
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[]\T1/zi4/m/n/9 tt <- data.frame(matrix(NA, nrow=3, ncol=3, dimnames=list(1:3,
paste("column", 1:3, sep="."))),[]
[56] [57]
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[][][]$\T1/zi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][]
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
11\T1/ptm/m/n/10 (2):R18
[58] [59] [60] [61]
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
[62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74]
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[][][]\T1/zi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
[75] [76] [77] [78] [79]
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[][][]$\T1/zi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
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[]\T1/zi4/m/n/9 predout <- claudinLow(x=train$xd, classes=as.matrix(train$clas
ses$Group,ncol=1), y=test$xd)[]
[8]
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[] \T1/zi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[]
[9] [10] [11] [12] [13]
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[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
[14] [15]
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
omics Con-sor-tium us-ing Affymetrix hgu133plus2
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[]\T1/ptm/m/n/10 International Ge-nomics Con-sor-tium, [][]$\T1/zi4/m/n/10 http
: / / www . intgen . org / research-[]services / biobanking-[]experience /
[16]
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e-sis, must be one of "two.sided"
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[18] [19] [20] [21] [22]
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
11\T1/ptm/m/n/10 (2):R18
[23]
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[]\T1/zi4/m/n/10 ihc4(ER, PGR, HER2, Ki67,age,size,grade,node,ana,scoreWithCli
nical=FALSE, na.rm = FALSE)[]
[24]
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[]\T1/zi4/m/n/9 ihc4(ER=sample(x=1:10, size=count,replace=TRUE),PGR=sample(x=1
:10, size=count,replace=TRUE),[]
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[]\T1/zi4/m/n/9 HER2=sample(x=0:1,size=count,replace=TRUE),Ki67=sample(x=1:100
, size=count,replace=TRUE),[]
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[]\T1/zi4/m/n/9 ihc4(ER=sample(x=1:10, size=count,replace=TRUE),PGR=sample(x=1
:10, size=count,replace=TRUE),[]
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[]\T1/zi4/m/n/9 HER2=sample(x=0:1,size=count,replace=TRUE),Ki67=sample(x=1:100
, size=count,replace=TRUE),[]
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[]\T1/zi4/m/n/9 age=demo.nkis[,"age"],size=demo.nkis[ ,"size"],grade=demo.nkis
[ ,"grade"],node=demo.nkis[ ,"node"],[]
[25] [26] [27] [28]
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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
and probes in columns,
[29]
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[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
named "En-trez-Gene.ID",
[30] [31] [32] [33] [34] [35] [36] [37] [38]
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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/zi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/zi4/m/n/10 do.mapping=TRUE
[39]
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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/zi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/zi4/m/n/10 do.mapping=TRUE
[40]
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[]\T1/zi4/m/n/9 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis,
gmap="entrezgene", do.mapping=TRUE)[]
[41]
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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/zi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/zi4/m/n/10 do.mapping=TRUE
[42]
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[]\T1/zi4/m/n/9 ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap
="entrezgene", do.mapping=TRUE)[]
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[]\T1/zi4/m/n/10 gmap = c("entrezgene", "ensembl_gene_id", "hgnc_symbol", "uni
gene", "refseq_mrna"),[]
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[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/zi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/zi4/m/n/10 do.mapping=TRUE
[43] [44]
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[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the
gene ex-pres-sions (see [][]\T1/zi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ).
[45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55]
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[]\T1/zi4/m/n/9 tt <- data.frame(matrix(NA, nrow=3, ncol=3, dimnames=list(1:3,
paste("column", 1:3, sep="."))),[]
[56] [57]
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[][][]$\T1/zi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][]
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
11\T1/ptm/m/n/10 (2):R18
[58] [59] [60] [61]
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
[62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74]
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[][][]\T1/zi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
[75] [76] [77] [78] [79]
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[][][]$\T1/zi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
[80] [81] (./Rd2.ind [82]
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)
(see the transcript file for additional information)pdfTeX warning (dest): name
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replaced by a fixed one
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[]\T1/zi4/m/n/9 predout <- claudinLow(x=train$xd, classes=as.matrix(train$clas
ses$Group,ncol=1), y=test$xd)[]
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[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
omics Con-sor-tium us-ing Affymetrix hgu133plus2
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[]\T1/ptm/m/n/10 International Ge-nomics Con-sor-tium, [][]$\T1/zi4/m/n/10 http
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
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[]\T1/zi4/m/n/10 ihc4(ER, PGR, HER2, Ki67,age,size,grade,node,ana,scoreWithCli
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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
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[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
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[]\T1/zi4/m/n/9 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis,
gmap="entrezgene", do.mapping=TRUE)[]
[41]
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[]\T1/zi4/m/n/9 ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap
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[]\T1/zi4/m/n/10 gmap = c("entrezgene", "ensembl_gene_id", "hgnc_symbol", "uni
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[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the
gene ex-pres-sions (see [][]\T1/zi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ).
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[]\T1/zi4/m/n/9 tt <- data.frame(matrix(NA, nrow=3, ncol=3, dimnames=list(1:3,
paste("column", 1:3, sep="."))),[]
[56] [57]
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[][][]$\T1/zi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][]
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
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[58] [59] [60] [61]
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
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[][][]\T1/zi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
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[][][]$\T1/zi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
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