topTable "resort.by" broken...
1
0
Entering edit mode
Jenny Drnevich ★ 2.2k
@jenny-drnevich-382
Last seen 8.1 years ago
HI, It appears that when colnames of the topTable output changed from "M" to "logFC", etc., the resort.by argument was not completely changed. The sort.by="M" and resort.by="A" arguments work fine, but not resort.by="M". See below for examples and sessionInfo(). I also had the same error trouble on another PC that had a fresh install of R 2.4.1 and everything else in March 2007, so I know it's not my R version. Thanks, Jenny > coef6 <- topTable(fit2,coef=6,number=100,resort.by="P") #works fine > coef6 <- topTable(fit2,coef=6,number=100,resort.by="A") #works fine > coef6 <- topTable(fit2,coef=6,number=100,sort.by="M") #works fine > coef6 <- topTable(fit2,coef=6,number=100,resort.by="M") Error in order(na.last, decreasing, ...) : argument 1 is not a vector > coef6 <- topTable(fit2,coef=6,number=100,resort.by="logFC") Error in match.argresort.by, c("M", "A", "P", "p", "T", "t", "B")) : 'arg' should be one of M, A, P, p, T, t, B > sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: affyQCReport simpleaffy made4 scatterplot3d ade4 "1.12.0" "2.8.0" "1.8.0" "0.3-24" "1.4-2" affyPLM affydata affycoretools annaffy xtable "1.10.0" "1.10.0" "1.7.5" "1.6.0" "1.4-3" gcrma matchprobes biomaRt RCurl XML "2.6.0" "1.6.0" "1.8.0" "0.7-0" "1.4-0" GOstats Category genefilter survival KEGG "2.0.3" "2.0.3" "1.12.0" "2.31" "1.14.1" RBGL annotate GO graph limma "1.10.0" "1.12.0" "1.14.1" "1.12.1" "2.9.13" affy affyio Biobase RWinEdt "1.12.1" "1.2.0" "1.12.2" "1.7-5" Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu
GO Survival Biobase annotate genefilter affy affydata graph gcrma matchprobes annaffy • 726 views
ADD COMMENT
0
Entering edit mode
@gordon-smyth
Last seen 3 hours ago
WEHI, Melbourne, Australia
Hi Jenny, Thanks for pointing this out. I've fixed it today in limma 2.9.16. Keep the reports coming. Best wishes Gordon At 02:20 AM 27/03/2007, Jenny Drnevich wrote: >HI, > >It appears that when colnames of the topTable output changed from >"M" to "logFC", etc., the resort.by argument was not completely >changed. The sort.by="M" and resort.by="A" arguments work fine, but >not resort.by="M". See below for examples and sessionInfo(). I also >had the same error trouble on another PC that had a fresh install of >R 2.4.1 and everything else in March 2007, so I know it's not my R version. > >Thanks, >Jenny > > > coef6 <- topTable(fit2,coef=6,number=100,resort.by="P") #works fine > > > coef6 <- topTable(fit2,coef=6,number=100,resort.by="A") #works fine > > > coef6 <- topTable(fit2,coef=6,number=100,sort.by="M") #works fine > > > coef6 <- topTable(fit2,coef=6,number=100,resort.by="M") >Error in order(na.last, decreasing, ...) : > argument 1 is not a vector > > > coef6 <- topTable(fit2,coef=6,number=100,resort.by="logFC") >Error in match.argresort.by, c("M", "A", "P", "p", "T", "t", "B")) : > 'arg' should be one of M, A, P, p, T, t, B > > > sessionInfo() >R version 2.4.0 (2006-10-03) >i386-pc-mingw32 > >locale: >LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >States.1252;LC_MONETARY=English_United >States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > >attached base packages: >[1] "splines" "tools" "methods" "stats" "graphics" "grDevices" >[7] "utils" "datasets" "base" > >other attached packages: > affyQCReport simpleaffy made4 scatterplot3d ade4 > "1.12.0" "2.8.0" "1.8.0" "0.3-24" "1.4-2" > affyPLM affydata affycoretools annaffy xtable > "1.10.0" "1.10.0" "1.7.5" "1.6.0" "1.4-3" > gcrma matchprobes biomaRt RCurl XML > "2.6.0" "1.6.0" "1.8.0" "0.7-0" "1.4-0" > GOstats Category genefilter survival KEGG > "2.0.3" "2.0.3" "1.12.0" "2.31" "1.14.1" > RBGL annotate GO graph limma > "1.10.0" "1.12.0" "1.14.1" "1.12.1" "2.9.13" > affy affyio Biobase RWinEdt > "1.12.1" "1.2.0" "1.12.2" "1.7-5" > >Jenny Drnevich, Ph.D. > >Functional Genomics Bioinformatics Specialist >W.M. Keck Center for Comparative and Functional Genomics >Roy J. Carver Biotechnology Center >University of Illinois, Urbana-Champaign > >330 ERML >1201 W. Gregory Dr. >Urbana, IL 61801 >USA > >ph: 217-244-7355 >fax: 217-265-5066 >e-mail: drnevich at uiuc.edu
ADD COMMENT

Login before adding your answer.

Traffic: 501 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6