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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 claudinLow(x,classes="",y,nGenes="",priors="equal",std=F,dist
m="euclidean",centroids=F)[]
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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/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 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",
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[]\T1/zi4/m/n/10 "pam50", "ssp2006", "ssp2003", "intClust", "AIMS","claudinLow
"), data, annot, do.mapping = 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 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis,
gmap="entrezgene", 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 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$[][]
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
11\T1/ptm/m/n/10 (2):R18
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
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[][][]\T1/zi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
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[][][]$\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 doo, Natchar Ratanasirigulchai, Markus S. Schroder, Laia Pare, J
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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 claudinLow(x,classes="",y,nGenes="",priors="equal",std=F,dist
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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/ptm/m/n/10 International Ge-nomics Con-sor-tium, [][]$\T1/zi4/m/n/10 http
: / / www . intgen . org / research-[]services / biobanking-[]experience /
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
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[]\T1/zi4/m/n/10 ihc4(ER, PGR, HER2, Ki67,age,size,grade,node,ana,scoreWithCli
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[]\T1/zi4/m/n/9 age=demo.nkis[,"age"],size=demo.nkis[ ,"size"],grade=demo.nkis
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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
and probes in columns,
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[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
named "En-trez-Gene.ID",
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[]\T1/zi4/m/n/9 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis,
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[]\T1/zi4/m/n/9 ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap
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[]\T1/zi4/m/n/10 gmap = c("entrezgene", "ensembl_gene_id", "hgnc_symbol", "uni
gene", "refseq_mrna"),[]
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[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the
gene ex-pres-sions (see [][]\T1/zi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ).
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[]\T1/zi4/m/n/9 tt <- data.frame(matrix(NA, nrow=3, ncol=3, dimnames=list(1:3,
paste("column", 1:3, sep="."))),[]
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[][][]$\T1/zi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][]
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
11\T1/ptm/m/n/10 (2):R18
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
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[][][]\T1/zi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
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[][][]$\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
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[]\T1/zi4/m/n/10 claudinLow(x,classes="",y,nGenes="",priors="equal",std=F,dist
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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-
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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, [][]$\T1/zi4/m/n/10 http
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[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
and probes in columns,
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[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
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[]\T1/zi4/m/n/9 ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap
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[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the
gene ex-pres-sions (see [][]\T1/zi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ).
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[]\T1/zi4/m/n/9 tt <- data.frame(matrix(NA, nrow=3, ncol=3, dimnames=list(1:3,
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[][][]$\T1/zi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
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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/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
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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
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[][][]$\T1/zi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
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[]\T1/zi4/m/n/10 claudinLow(x,classes="",y,nGenes="",priors="equal",std=F,dist
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[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
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[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
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[]\T1/ptm/m/n/10 International Ge-nomics Con-sor-tium, [][]$\T1/zi4/m/n/10 http
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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/zi4/m/n/9 ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap
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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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[][][]$\T1/zi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
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\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
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[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
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[][][]\T1/zi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 intrinsic.clu
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[][][]$\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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exlive/2016/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/te
xlive/2016/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2
016/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2016/texmf-
dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts
/type1/urw/times/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/urw
/times/utmri8a.pfb>
Output written on Rd2.pdf (85 pages, 291367 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/Rtmp70K5mz/Rbuild31f338c6942e/genefu/build/genefu.pdf’ ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘genefu_2.14.0.tar.gz’
