Hi All, I aligned my RNA-seq data using ensemble igenome for cattle and used edgeR for DE identification. I wanted to use goseq but I got this error: >pwf=nullp(genes,"bosTau4","ensGene") Loading bosTau4 length data... Error in qr.R(qrx) : could not find symbol "..." in environment of the generic function. I have my gene_id as ENSBTAG00000000005 but in the package, I realised it's in ENSG00000230758 (ENSBTAG and ENSG) This is the first time as I don't have much experience in converting my gene_id to the "ENSG" format which appears to be compatible with goseq. I'm not sure about this as I'm a newbie. Thanks and I appreciate any imput. -- output of sessionInfo(): > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] goseq_1.10.0 geneLenDataBase_0.99.10 BiasedUrn_1.05 [4] edgeR_3.0.8 limma_3.14.4 loaded via a namespace (and not attached): [1] AnnotationDbi_1.20.7 Biobase_2.18.0 BiocGenerics_0.4.0 [4] biomaRt_2.14.0 Biostrings_2.26.3 bitops_1.0-5 [7] BSgenome_1.26.1 DBI_0.2-5 GenomicFeatures_1.10.2 [10] GenomicRanges_1.10.7 grid_2.15.2 IRanges_1.16.6 [13] lattice_0.20-10 Matrix_1.0-12 mgcv_1.7-22 [16] nlme_3.1-105 parallel_2.15.2 RColorBrewer_1.0-5 [19] RCurl_1.95-4.1 Rsamtools_1.10.2 RSQLite_0.11.2 [22] rtracklayer_1.18.2 stats4_2.15.2 tools_2.15.2 [25] XML_3.96-1.1 xtable_1.7-1 zlibbioc_1.4.0 > -- Sent via the guest posting facility at bioconductor.org.

Yemmy [guest] <guest at="" ...=""> writes: > I aligned my RNA-seq data using ensemble igenome for cattle and used edgeR for DE identification. I wanted > to use goseq but I got this error: > > >pwf=nullp(genes,"bosTau4","ensGene") > Loading bosTau4 length data... > Error in qr.R(qrx) : > could not find symbol "..." in environment of the generic function. > > I have my gene_id as ENSBTAG00000000005 but in the package, I realised it's in ENSG00000230758 (ENSBTAG > and ENSG) This is the first time as I don't have much experience in converting my gene_id to the "ENSG" > format which appears to be compatible with goseq. I'm not sure about this as I'm a newbie. > > Thanks and I appreciate any imput. Hi, The cattle ensembl ids should work fine for goseq. I just did a small test on my version of goseq and couldn't reproduce the error you posted. The ENSG genes are just for human I think, so shouldn't be mixed with the cattle ones. It could be that there is some other issue with the gene names. If you email me a file with the list from "names(genes)" I can look into it in more detail. Cheers, Nadia.