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* checking for file ‘genefu/DESCRIPTION’ ... OK
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\T1/ptm/m/n/10 Kains \T1/zi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/zi4/m/n/10 <markus.schroeder@ucdconnect.ie>
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[] \T1/zi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[]
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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/zi4/m/n/10 fuzzy.ttest(x, w1, w2, alternative=c("two.sided", "less", "gr
eater"), check.w = TRUE, na.rm = FALSE)[]
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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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[][][]$\T1/zi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
[]$http : / / www . nicebread . de / blog / files / fc02e1635792cb0f2b3cbd1f7e6
c580b-[]10 .
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[]\T1/zi4/m/n/9 randst <- apply(rands, 1, function(x, xx, ww1, ww2) { return(f
uzzy.ttest(x=xx, w1=ww1[x], w2=ww2[x])[2]) }, xx=xx, ww1=ww1, ww2=ww2)[]
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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 map.datasets(datas, annots, do.mapping = FALSE, mapping.coln
= "EntrezGene.ID", mapping, verbose = FALSE)[]
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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,
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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",
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[]\T1/zi4/m/n/10 ovcAngiogenic(data, annot, hgs, gmap = c("entrezgene", "ensem
bl_gene_id", "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[]
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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
[30]
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[]\T1/zi4/m/n/9 ovcAngiogenic.nkis <- ovcAngiogenic(data=data.nkis, annot=anno
t.nkis, gmap="entrezgene", do.mapping=TRUE)[]
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[]\T1/zi4/m/n/10 ovcCrijns(data, annot, hgs, gmap = c("entrezgene", "ensembl_g
ene_id", "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[]
[31]
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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
[32]
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[]\T1/zi4/m/n/9 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis,
gmap="entrezgene", do.mapping=TRUE)[]
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[]\T1/zi4/m/n/10 ovcTCGA(data, annot, gmap = c("entrezgene", "ensembl_gene_id"
, "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[]
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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 ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap
="entrezgene", do.mapping=TRUE)[]
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[]\T1/zi4/m/n/10 ovcYoshihara(data, annot, hgs, gmap = c("entrezgene", "ensemb
l_gene_id", "hgnc_symbol", "unigene", "refseq_mrna"), do.mapping = FALSE, verbo
se = FALSE)[]
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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
[34]
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[]\T1/zi4/m/n/9 ovcYoshihara.nkis <- ovcYoshihara(data=data.nkis, annot=annot.
nkis, gmap="entrezgene", do.mapping=TRUE)[]
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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="."))), stringsAsFactors=FALSE)[]
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[]\T1/zi4/m/n/9 tt <- setcolclass.df(df=tt, colclass=c("numeric", "factor", "c
haracter"), factor.levels=list(NULL, c("F1", "F2", "F3"), NULL))[]
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[][][]$\T1/zi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][]
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
11\T1/ptm/m/n/10 (2):R18
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
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[][][]\T1/zi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
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[][][]$\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/ptm/m/n/10 Kains \T1/zi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/zi4/m/n/10 <markus.schroeder@ucdconnect.ie>
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[] \T1/zi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[]
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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/zi4/m/n/10 fuzzy.ttest(x, w1, w2, alternative=c("two.sided", "less", "gr
eater"), check.w = TRUE, na.rm = FALSE)[]
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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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[][][]$\T1/zi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
[]$http : / / www . nicebread . de / blog / files / fc02e1635792cb0f2b3cbd1f7e6
c580b-[]10 .
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[]\T1/zi4/m/n/9 randst <- apply(rands, 1, function(x, xx, ww1, ww2) { return(f
uzzy.ttest(x=xx, w1=ww1[x], w2=ww2[x])[2]) }, xx=xx, ww1=ww1, ww2=ww2)[]
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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 map.datasets(datas, annots, do.mapping = FALSE, mapping.coln
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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,
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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",
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[]\T1/zi4/m/n/10 ovcAngiogenic(data, annot, hgs, gmap = c("entrezgene", "ensem
bl_gene_id", "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[]
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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 ovcAngiogenic.nkis <- ovcAngiogenic(data=data.nkis, annot=anno
t.nkis, gmap="entrezgene", do.mapping=TRUE)[]
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[]\T1/zi4/m/n/10 ovcCrijns(data, annot, hgs, gmap = c("entrezgene", "ensembl_g
ene_id", "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[]
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[]\T1/zi4/m/n/9 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis,
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[]\T1/zi4/m/n/10 ovcTCGA(data, annot, gmap = c("entrezgene", "ensembl_gene_id"
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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 ovcYoshihara(data, annot, hgs, gmap = c("entrezgene", "ensemb
l_gene_id", "hgnc_symbol", "unigene", "refseq_mrna"), do.mapping = FALSE, verbo
se = FALSE)[]
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[]\T1/zi4/m/n/9 ovcYoshihara.nkis <- ovcYoshihara(data=data.nkis, annot=annot.
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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="."))), stringsAsFactors=FALSE)[]
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[]\T1/zi4/m/n/9 tt <- setcolclass.df(df=tt, colclass=c("numeric", "factor", "c
haracter"), factor.levels=list(NULL, c("F1", "F2", "F3"), NULL))[]
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[][][]$\T1/zi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][]
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
11\T1/ptm/m/n/10 (2):R18
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
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[][][]\T1/zi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
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[][][]$\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/ptm/m/n/10 Kains \T1/zi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/zi4/m/n/10 <markus.schroeder@ucdconnect.ie>
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[] \T1/zi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[]
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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/zi4/m/n/10 fuzzy.ttest(x, w1, w2, alternative=c("two.sided", "less", "gr
eater"), check.w = TRUE, na.rm = FALSE)[]
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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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[][][]$\T1/zi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
[]$http : / / www . nicebread . de / blog / files / fc02e1635792cb0f2b3cbd1f7e6
c580b-[]10 .
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[]\T1/zi4/m/n/9 randst <- apply(rands, 1, function(x, xx, ww1, ww2) { return(f
uzzy.ttest(x=xx, w1=ww1[x], w2=ww2[x])[2]) }, xx=xx, ww1=ww1, ww2=ww2)[]
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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 map.datasets(datas, annots, do.mapping = FALSE, mapping.coln
= "EntrezGene.ID", mapping, verbose = FALSE)[]
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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,
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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",
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[]\T1/zi4/m/n/10 ovcAngiogenic(data, annot, hgs, gmap = c("entrezgene", "ensem
bl_gene_id", "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[]
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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
[32]
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[]\T1/zi4/m/n/9 ovcAngiogenic.nkis <- ovcAngiogenic(data=data.nkis, annot=anno
t.nkis, gmap="entrezgene", do.mapping=TRUE)[]
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[]\T1/zi4/m/n/10 ovcCrijns(data, annot, hgs, gmap = c("entrezgene", "ensembl_g
ene_id", "hgnc_symbol", "unigene"), do.mapping = FALSE, verbose = FALSE)[]
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tm/m/n/10 at-tribute to use for map-ping if \T1/zi4/m/n/10 do.mapping=TRUE
[34]
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[]\T1/zi4/m/n/9 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis,
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[]\T1/zi4/m/n/10 ovcTCGA(data, annot, gmap = c("entrezgene", "ensembl_gene_id"
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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 ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap
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[]\T1/zi4/m/n/10 ovcYoshihara(data, annot, hgs, gmap = c("entrezgene", "ensemb
l_gene_id", "hgnc_symbol", "unigene", "refseq_mrna"), do.mapping = FALSE, verbo
se = FALSE)[]
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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 ovcYoshihara.nkis <- ovcYoshihara(data=data.nkis, annot=annot.
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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="."))), stringsAsFactors=FALSE)[]
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[]\T1/zi4/m/n/9 tt <- setcolclass.df(df=tt, colclass=c("numeric", "factor", "c
haracter"), factor.levels=list(NULL, c("F1", "F2", "F3"), NULL))[]
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[][][]$\T1/zi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][]
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
11\T1/ptm/m/n/10 (2):R18
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
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[][][]\T1/zi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
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[][][]$\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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