[BioC] topTable "resort.by" broken...

[Gordon Smyth]

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.arg(resort.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