[BioC] question about limma2annaffy

[Jenny Drnevich]

Hi Jim,

I'm learning to use your limma2annaffy function, and I have a few 
questions. In the affycoretools vignette (Feb 6, 2007), you call 
limma2annaffy this way:

 > limma2annaffy(eset, fit2, design, annotation(eset), pfilt = 0.05)

I think there's a typo in this, because you've left out the contrast 
matrix. When I try the same on my data:

 > limma2annaffy(gcrma.pres, fit2, design, annotation(gcrma.pres),pfilt=0.05)
Error in vector("list", dim(contrast)[2]) :
         negative length vectors are not allowed

When I try naming the annotation(gcrma.pres) argument, I get this:

 > limma2annaffy(gcrma.pres, fit2, design, 
lib=annotation(gcrma.pres),pfilt=0.05)
Error in vector("list", dim(contrast)[2]) :
         argument "contrast" is missing, with no default

It does work when I add the contrast matrix:

 > limma2annaffy(gcrma.pres, fit2, design, 
cont.matrix,annotation(gcrma.pres),pfilt=0.05)


So, besides pointing out an apparent error in the vignette, I had a 
question as to what you would do if you didn't use a contrast matrix? Now, 
most all the time that I analyze affy data I do use a contrast matrix, but 
you don't always have to use one. I have some other questions/suggestions 
to improve the ease of use of affycoretools, but they are too complicated 
to put in this e-mail...

Thanks,
Jenny

 > sessionInfo()
R version 2.5.0 Under development (unstable) (2007-02-03 r40636)
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"     "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "methods"   "base"

other attached packages:
       canine2  affyQCReport       lattice   geneplotter  RColorBrewer
     "1.15.13"     "1.13.16"     "0.14-16"      "1.12.0"       "0.2-3"
    simpleaffy         made4 scatterplot3d          ade4       affyPLM
       "2.9.1"       "1.8.0"      "0.3-24"       "1.4-2"     "1.11.13"
      affydata affycoretools       annaffy        xtable         gcrma
      "1.11.1"       "1.7.7"       "1.7.2"       "1.4-3"       "2.7.1"
   matchprobes       biomaRt         RCurl           XML       GOstats
       "1.7.4"      "1.9.16"       "0.8-0"       "1.4-1"      "2.1.11"
      Category    genefilter      survival          KEGG          RBGL
      "2.1.11"      "1.13.8"        "2.31"      "1.15.1"      "1.11.4"
      annotate            GO         graph         limma          affy
      "1.13.6"      "1.15.1"      "1.13.5"      "2.9.10"     "1.13.14"
        affyio       Biobase       RWinEdt
       "1.3.3"     "1.13.36"       "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