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

[Jenny Drnevich]

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