[BioC] goseq error messsage

[Nadia Davidson]

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.