Dear Matthew, I am getting the following error when using goseq. Any idea what may cause it? Thanks, Adi > pwf=nullp(genes,bias.data=cntbias) > gocats=as.list(org.Hs.egGO2ALLEGS) > GOr=goseq(pwf,gene2cat=gocats) Using manually entered categories. Calculating the p-values... Error in dWNCHypergeo(num_de_incat, num_incat, num_genes - num_incat, : Negative parameter > head(pwf) DEgenes bias.data pwf 642819 0 3764 0.05775376 414235 0 124 0.02107342 57107 0 14702 0.06023892 649159 1 248 0.02542837 3127 0 44633 0.06357525 100507412 1 1337 0.05268580 > head(gocats[3:5]) $`GO:0000012` IDA IDA IEA IMP IDA IDA "3981" "7141" "7515" "23411" "54840" "55775" IMP IMP IEA "55775" "200558" "100133315" $`GO:0000018` IEA IEA IMP IEA IEA IDA IDA IEA "604" "641" "641" "940" "958" "1111" "2956" "3458" IEA ISS TAS TAS NAS TAS TAS IEA "3558" "3565" "3565" "3575" "3586" "3836" "3838" "4292" TAS IBA IDA ISS IDA IMP IMP IEA "4361" "4436" "4436" "4436" "4437" "5531" "6118" "6778" IDA IEA IDA IEA IDA IEA ISS ISS "7040" "7320" "8741" "9466" "10111" "11105" "22976" "23529" IEA IBA IDA IMP ISS IMP IEA IEA "30009" "50943" "51548" "51750" "54386" "55010" "56154" "56852" IEP IMP IEA IMP "56916" "56979" "80762" "151987" $`GO:0000019` IEA IEA TAS IDA "641" "4292" "4361" "10111" > sessionInfo() R version 2.15.3 RC (2013-02-24 r62054) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] KEGG.db_2.8.0 goseq_1.10.0 geneLenDataBase_0.99.10 [4] BiasedUrn_1.05 GO.db_2.8.0 GOstats_2.24.0 [7] graph_1.36.2 Category_2.24.0 org.Hs.eg.db_2.8.0 [10] RSQLite_0.11.2 DBI_0.2-5 BiocInstaller_1.8.3 [13] edgeR_3.0.8 limma_3.14.4 rtracklayer_1.18.2 [16] multicore_0.1-7 Rsamtools_1.10.2 Biostrings_2.26.3 [19] GenomicFeatures_1.11.13 AnnotationDbi_1.20.6 Biobase_2.18.0 [22] GenomicRanges_1.11.31 IRanges_1.17.35 BiocGenerics_0.5.6 loaded via a namespace (and not attached): [1] annotate_1.36.0 AnnotationForge_1.0.3 biomaRt_2.14.0 [4] bitops_1.0-5 BSgenome_1.26.1 genefilter_1.40.0 [7] grid_2.15.3 GSEABase_1.20.2 lattice_0.20-13 [10] Matrix_1.0-11 mgcv_1.7-22 nlme_3.1-108 [13] RBGL_1.34.0 RCurl_1.95-4.1 splines_2.15.3 [16] stats4_2.15.3 survival_2.37-4 tools_2.15.3 [19] XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.4.0 Adi Laurentiu TARCA, Ph.D. Assistant Professor (Research), Department of Computer Science & Center for Molecular Medicine and Genetics, Wayne State University, Director, Bioinformatics and Computational Biology Unit, Perinatology Research Branch (NICHD), 3990 John R., Office 4809, Detroit, Michigan 48201 Tel: 1-313-5775305 [[alternative HTML version deleted]]

Tarca, Adi <atarca at="" ...=""> writes: > > Dear Matthew, > I am getting the following error when using goseq. Any idea what may cause it? > Thanks, > Adi > > > pwf=nullp(genes,bias.data=cntbias) > > gocats=as.list(org.Hs.egGO2ALLEGS) > > GOr=goseq(pwf,gene2cat=gocats) > Using manually entered categories. > Calculating the p-values... > Error in dWNCHypergeo(num_de_incat, num_incat, num_genes - num_incat, : > Negative parameter > > head(pwf) > DEgenes bias.data pwf > 642819 0 3764 0.05775376 > 414235 0 124 0.02107342 > 57107 0 14702 0.06023892 > 649159 1 248 0.02542837 > 3127 0 44633 0.06357525 > 100507412 1 1337 0.05268580 > > head(gocats[3:5]) > $`GO:0000012` > IDA IDA IEA IMP IDA IDA > "3981" "7141" "7515" "23411" "54840" "55775" > IMP IMP IEA > "55775" "200558" "100133315" > > Adi Laurentiu TARCA, Ph.D. Dear Adi, I think the trouble is that "org.Hs.egGO2ALLEGS" lists some GO groups twice for the same gene. This is making goseq overestimate the number of genes in a particular GO category, to the extent that the number of genes in the category is more than the total number of genes. It should be simple to fix with: gocats<-sapply(gocats,function(x){unique(x)}) before the "goseq" command. I'll update the goseq code so it checks for this scenario in future. Cheers, Nadia.