Hi Jim, Thanks for getting back to me. On Mon, 2008-06-23 at 09:18 -0400, James W. MacDonald wrote: > Hi Peadar, > > Peadar ? 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? vennSelect behaves exactly that way if I feed it more than 3 contrasts. What I've been doing is subsetting the TestResults and contrast matrix to the two contrasts I want to look at eg: vennSelect(gcrma_Data, design, interday_res[,c("pregHi_d5vd7", "pregLo_d5vd7")], interday.contrasts[,c("pregHi_d5vd7", "pregLo_d5vd7")], interday_fit2, stat="tstat") where pregHi_d5vd7 and pregLo_d5vd7 are contrasts of interest. Having written this, I've just found that the problem was indeed passing in the entire fit object. Subsetting this as well corrects the issue. I had tried and failed to do that before but I guess I had a typo in the command. Anyway, I just thought I should finish this out in case anybody checking the archives in the future has a similar question. so the correct call should have been: vennSelect(gcrma_Data, design, interday_res[,c("pregHi_d5vd7", "pregLo_d5vd7")], interday.contrasts[,c("pregHi_d5vd7", "pregLo_d5vd7")],interday_fit2[,c("pregHi_d5vd7", "pregLo_d5vd7")], stat="tstat") Go raibh m?le maith agat Jim, Peadar > > > > > 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=e n_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.U TF-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" > > >