[BioC] goseq error messsage

[Yemmy [guest]]

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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