[BioC] affycoretools vennSelect problem

[James W. MacDonald]

Hi Peadar,

Peadar Ó Gaora wrote:
> 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.

If you have more than three contrasts, vennSelect() is supposed to error 
out with a message - is that not happening?

> 
> 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?

I haven't made many changes to affycoretools for a while, but that 
version of R/BioC is seriously ancient. The first step should be to 
upgrade to R-2.7.1 and BioC 2.2.

Then you should show the code you are using (hopefully simplified if 
possible).

Best,

Jim



> 
> 
> 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"
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623