Hi All, Using goSeq to analyze two gene lists - up regulated and down regulated genes generated with edgeR, the up regulated list seems good, but there is an error with down regulated list. Couldn't figure out what's wrong with it. Please refer to the command line and output below. Thanks very for me for help. Steve # up list > lateTrans524up.pwf <- nullp(lateTrans524.up.vector, bias.data=hs.glen.assayed, plot.fit=FALSE) > lateTrans524up.goWall <- goseq(lateTrans524up.pwf, gene2cat=hs.go, test.cats=c("GO:CC", "GO:BP", "GO:MF")) Using manually entered categories. Calculating the p-values... > head(lateTrans524up.goWall) > lateTrans524up.goSamp <- goseq(lateTrans524up.pwf, gene2cat=hs.go, method="Sampling", repcnt=1000) Using manually entered categories. Running the simulation... Calculating the p-values... 100 % g the p-values... > head(lateTrans524up.goSamp) # down list > lateTrans524dn.pwf <- nullp(lateTrans524.dn.vector, bias.data=hs.glen.assayed, plot.fit=FALSE) > lateTrans524dn.goWall <- goseq(lateTrans524dn.pwf, gene2cat=hs.go, test.cats=c("GO:CC", "GO:BP", "GO:MF")) Using manually entered categories. Calculating the p-values... Error in dWNCHypergeo(subcount, totcount, N - totcount, n, weight) : Invalid value for odds > lateTrans524dn.goSamp <- goseq(lateTrans524dn.pwf, gene2cat=hs.go, method="Sampling", repcnt=1000) Using manually entered categories. Running the simulation... Calculating the p-values... 100 % g the p-values... > head(lateTrans524dn.goSamp) > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GO.db_2.4.5 RSQLite_0.9-4 DBI_0.2-5 AnnotationDbi_1.12.0 Biobase_2.10.0 edgeR_2.0.5 [7] goseq_1.2.0 geneLenDataBase_0.99.5 BiasedUrn_1.03 loaded via a namespace (and not attached): [1] Biostrings_2.18.4 BSgenome_1.18.3 GenomicRanges_1.2.3 grid_2.12.1 IRanges_1.8.9 lattice_0.19-30 limma_3.6.9 [8] Matrix_0.999375-50 mgcv_1.7-6 nlme_3.1-98 RCurl_1.6-6 rtracklayer_1.10.6 tools_2.12.1 XML_3.2-0 [[alternative HTML version deleted]]

Hi, On Sun, Oct 30, 2011 at 6:10 PM, steve Shen <shen.sq at="" gmail.com=""> wrote: > Hi All, > > Using goSeq to analyze two gene lists - up regulated and down regulated > genes generated with edgeR, the up regulated list seems good, but there is > an error with down regulated list. Couldn't figure out what's wrong with > it. Please refer to the command line and output below. Thanks very for me > for help. Not sure what's wrong with it either, but your sessionInfo shows that you are using a (1) old version of R (2.12.1), and therefore (2) an old version of goseq. I would suggest upgrading to the newest R/Bioconductor/goseq combo to see if the error is still there. The slightly unfortunate thing for you is that R 2.14.0 is also scheduled to come out tomorrow so if you choose to upgrade to R 2.13.x, you will have the latest and greatest for < 24 hrs. The upgrade process isn't all that burdensome, so no big deal, but you might consider updating straight to the version of 2.14 that you can get from the link below as 2.14-branch: http://r.research.att.com/ > Steve You said it, brother. -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact