After using edgeR to find differentially expressed genes, I tried to follow the instructions in goseq to correct for length bias. top$table[1:10,1] [1] "ENSG00000138131" "ENSG00000204616" "ENSG00000204876" "ENSG00000118972" "ENSG00000143546" "ENSG00000163993" "ENSG00000012223" "ENSG00000188257" [9] "ENSG00000140403" "ENSG00000059804" geneLengths=getlength(top$table[,1],'hg19','ensGene') geneLengths[1:10] [1] 3672.0 2033.5 2675.5 3021.0 454.0 512.0 1813.0 911.5 2877.0 3504.0 (so far, so good) pwf=nullp(top$table[,1],'hg19','ensGene') Loading hg19 length data... Error in if (matched_frac == 0) { : missing value where TRUE/FALSE needed > sessionInfo() R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] tools grid stats graphics grDevices utils datasets methods base other attached packages: [1] goseq_1.2.0 geneLenDataBase_0.99.5 BiasedUrn_1.03 qvalue_1.24.0 sagenhaft_1.20.0 SparseM_0.86 [7] edgeR_2.0.5 hexbin_1.24.1 DESeq_1.2.1 locfit_1.5-6 lattice_0.19-17 akima_0.5-4 [13] Biobase_2.10.0 loaded via a namespace (and not attached): [1] annotate_1.28.1 AnnotationDbi_1.12.0 Biostrings_2.18.4 BSgenome_1.18.3 DBI_0.2-5 genefilter_1.32.0 [7] geneplotter_1.28.0 GenomicRanges_1.2.3 IRanges_1.8.9 limma_3.6.9 Matrix_0.999375-46 mgcv_1.7-3 [13] nlme_3.1-98 RColorBrewer_1.0-2 RCurl_1.5-0.1 RSQLite_0.9-4 rtracklayer_1.10.6 splines_2.12.2 [19] survival_2.36-5 tcltk_2.12.2 XML_3.2-0.2 xtable_1.5-6 >

Got it. I needed an indicator variable for which genes on in the gene list - not the actual gene list. (Amazing how reading the manual carefully can help!) --Naomi At 10:10 AM 3/28/2011, Naomi Altman wrote: >After using edgeR to find differentially expressed genes, I tried to >follow the instructions in goseq to correct for length bias. > > > top$table[1:10,1] > [1] "ENSG00000138131" "ENSG00000204616" "ENSG00000204876" > "ENSG00000118972" "ENSG00000143546" "ENSG00000163993" > "ENSG00000012223" "ENSG00000188257" > [9] "ENSG00000140403" "ENSG00000059804" >geneLengths=getlength(top$table[,1],'hg19','ensGene') >geneLengths[1:10] > [1] 3672.0 2033.5 2675.5 3021.0 454.0 512.0 1813.0 911.5 2877.0 3504.0 > >(so far, so good) > >pwf=nullp(top$table[,1],'hg19','ensGene') >Loading hg19 length data... >Error in if (matched_frac == 0) { : missing value where TRUE/FALSE needed > > > sessionInfo() >R version 2.12.2 (2011-02-25) >Platform: i386-pc-mingw32/i386 (32-bit) > >locale: >[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >States.1252 LC_MONETARY=English_United States.1252 >[4] LC_NUMERIC=C LC_TIME=English_United States.1252 > >attached base packages: >[1] tools grid stats graphics grDevices >utils datasets methods base > >other attached packages: > [1] goseq_1.2.0 geneLenDataBase_0.99.5 > BiasedUrn_1.03 qvalue_1.24.0 sagenhaft_1.20.0 SparseM_0.86 > [7] edgeR_2.0.5 hexbin_1.24.1 DESeq_1.2.1 > locfit_1.5-6 lattice_0.19-17 akima_0.5-4 >[13] Biobase_2.10.0 > >loaded via a namespace (and not attached): > [1] annotate_1.28.1 AnnotationDbi_1.12.0 > Biostrings_2.18.4 BSgenome_1.18.3 DBI_0.2-5 genefilter_1.32.0 > [7] geneplotter_1.28.0 GenomicRanges_1.2.3 IRanges_1.8.9 > limma_3.6.9 Matrix_0.999375-46 mgcv_1.7-3 >[13] nlme_3.1-98 RColorBrewer_1.0-2 RCurl_1.5-0.1 >RSQLite_0.9-4 rtracklayer_1.10.6 splines_2.12.2 >[19] survival_2.36-5 tcltk_2.12.2 XML_3.2-0.2 xtable_1.5-6 > > > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor