Dear Paedar, I don't actually know the Vennselect wrapper but I find that when I export contrasts of Venn diagrams from Limma I always get the FULL diagram (e.g. 1, 0, -1, 0, 1) for each probe set on my chip and in the order of the imported genelist. I presume this is so I can safely "reattach" the annotations, expression levels and all sorts of other info which is missing from the Venntable, and this is precisely what I use it for. Subsequent ordering by p-value, contrast, contrast combinations, in the spreadsheet program of choice allows me to follow up on all sorts of subsets. So I assume you will find Vennselect provides the full list, just like my "old" version. If you don't want the rest- you can always delete it ;-) If you only got the selected genes (some of) the annotation might possibly still be present, but I certainly don't want to be the one who re- inserts all the extra information I had before I imported the file into R/BioC. Not if there are more than a few genes and I tend to get 100s. Also I find it interesting to see that e.g. geneX only JUST falls out of my cutoff etc. Best regards, Nick ------------------------------ Message: 2 Date: Mon, 23 Jun 2008 12:50:19 +0000 From: Peadar ? Gaora <peadar.ogaora@ucd.ie> Subject: [BioC] affycoretools vennSelect problem To: bioconductor at stat.math.ethz.ch Message-ID: <1214225419.25084.111.camel at pogpc.ucd.ie> Content-Type: text/plain; charset=ISO-8859-15 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_NAM E=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_IE.UTF-8;LC_IDENTIFI CATION =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 ? Gaora UCD Conway Institute, Belfield, Dublin 4. (01) 716-6915 ############################