[BioC] affycoretools vennSelect problem

[Peadar Ó Gaora]

Hello BioCer's,

I've been using affycoretools, particularly limma2annaffy,for a while
now and love it.  These wrappers really make life simpler.

However (there was bound to be a however), in a recent experiment I've
had some problems with vennSelect.  The experiment has 4 groups and 4
time points, 5 replicates each.  There are then, a plethora of possible
contrasts of interest.  I've run one particular analysis with 34
contrasts and wanted to look at the unique (differentially expressed,
p<0.05) genes and intersections between some of them.  When I use
vennSelect to do this, it returns probesets with P values well above
0.05.

I can't see where it is picking these from as the lists from the
individual contrasts all look perfectly fine (P-value for all selected
genes < 0.05).  I have tried subsetting the TestResults and contrasts
matrices in the call to vennSelect.  I've also tried generating new ones
TestResults objext and contrast matrix which include only the
comparisons being analysed.  The fit object however contains the entire
dataset.  Could this be where things are going wrong?


Any help much appreciated.

Peadar


> sessionInfo()
R version 2.5.1 (2007-06-27)
ia64-unknown-linux-gnu

locale:
LC_CTYPE=en_IE.UTF-8;LC_NUMERIC=C;LC_TIME=en_IE.UTF-8;LC_COLLATE=en_IE.UTF-8;LC_MONETARY=en_IE.UTF-8;LC_MESSAGES=en_IE.UTF-8;LC_PAPER=en_IE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_IE.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices"
"datasets"
[7] "utils"     "methods"   "base"

other attached packages:
affycoretools       annaffy        xtable         gcrma   matchprobes
      "1.8.1"       "1.8.1"       "1.5-1"       "2.8.1"       "1.8.1"
      biomaRt         RCurl           XML       GOstats      Category
     "1.10.1"       "0.8-0"      "1.92-1"       "2.2.6"       "2.2.3"
       Matrix       lattice    genefilter      survival          KEGG
 "0.999375-2"     "0.15-11"      "1.14.1"        "2.32"      "1.16.1"
         RBGL      annotate            GO         graph         limma
     "1.12.0"      "1.14.1"      "1.16.0"      "1.14.2"      "2.10.5"
         affy        affyio       Biobase
     "1.14.2"       "1.4.1"      "1.14.1"

-- 


############################
Dr. Peadar Ó Gaora
UCD Conway Institute,
Belfield,
Dublin 4.

(01) 716-6915
############################