Hello,

I have the list of gene IDs which are ensembl Ids I wanted do GO analysis for this list of genes. How can I do this from the GOseq I went through vignette which is running the GOseq from the DE genes output, my genes list are not from the DE this are obtained according to my objective.

can anyone suggest me?

Gene IDs list is looking as

ENSMUSG00000061111

ENSMUSG00000062761

ENSMUSG00000063445

ENSMUSG00000066705

ENSMUSG00000070372

ENSMUSG00000073411

ENSMUSG00000073684

ENSMUSG00000074182

ENSMUSG00000078453

code What I have run data containes the above listed gene name

        gene=read.table("data", header=T)
        gene<- gene$gene_name
        pwf=nullp(gene,"mm10","ensGene")

Error what I got

        Can't find mm10/ensGene length data in genLenDataBase...
        A TxDb annotation package exists for mm10. Consider installing it to get the gene lengths.
       Trying to download from UCSC. This might take a couple of minutes. 
       Error in value[[3L]](cond) : 
       Length information for genome mm10 and gene ID ensGene is not available. You will have to specify bias.data manually.
       In addition: Warning messages:
       1: In library() :
       libraries ‘/usr/local/lib/R/site-library’, ‘/usr/lib/R/site-library’ contain no packages
      2: In grep(txdbPattern, installedPackages) :
      argument 'pattern' has length > 1 and only the first element will be used

Thank you

So when you tried what you tried, you got this message:

Can't find mm10/ensGene length data in genLenDataBase...
A TxDb annotation package exists for mm10. Consider installing it to get the gene lengths.
Trying to download from UCSC. This might take a couple of minutes. 
Error in value[[3L]](cond) : 
Length information for genome mm10 and gene ID ensGene is not available. You will have to specify bias.data manually.

It's important to read and try to understand the error and warning messages that you get. Basically this is saying that the attempt to get the gene lengths automatically has failed and that you will have to specify these data manually. In general I think this is a pretty clear message?

If you haven't read the vignette, you should do so, particularly section 5.3, which covers this issue. Anyway, it says to do this

> tx <- transcriptsBy(TxDb.Mmusculus.UCSC.mm10.ensGene)
> ld <- median(width(tx))
> head(ld)
ENSMUSG00000000001 ENSMUSG00000000003 ENSMUSG00000000028 ENSMUSG00000000031 
           38867.0            15676.0            31174.0             1589.0 
ENSMUSG00000000037 ENSMUSG00000000049 
           95425.0            22637.5

And from ?nullp, there is this

bias.data: A numeric vector containing the data on which the DE may
          depend.  Usually this is the median transcript length of each
          gene in bp.  If set to 'NULL' 'nullp' will attempt to fetch
          length using 'getlength'.

So that's how you should figure out what you need, and how you get it. Knowing how to do that sort of thing is a necessary skill if you want to be able to use R or Bioconductor well, so it's worth learning.