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

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