[BioC] goseq error messsage
Yemmy [guest]
guest at bioconductor.org
Wed Apr 17 02:35:21 CEST 2013
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
>
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