Hi Divya,

The organism packages do not keep any information on gene length, so goseq
obtains it from the UCSC.  As you have noted, this is not available for
Arabidopsis.  Unfortunately, this means you will have to obtain this
information from elsewhere and format it for use with goseq.  Information on
formatting length data is available in the help for the nullp function and
in the vignette, but in short you need to give the bias.data argument a
vector the same length as your DEgenes vector which contains the length of
each gene.

Cheers,

Matt

On Mon, Sep 12, 2011 at 10:54 AM, Divya, D. <D.Divya@uu.nl> wrote:

> Hi,
>
> I want to do the GO analysis for Arabidopsis using GOseq package. From the
> PDF I understood that the package relies on the UCSC genome browser to
> extract information regarding gene length, GO category. But UCSC genome
> browser has information about animal kingdom and I am unable to add
> Arabidopsis genome information which is available from TAIR.
>
> I have used "org.At.tair.db<
> http://www.bioconductor.org/packages/release/data/annotation/html/org.At.tair.db.html>"
> but this doesn't add information regarding gene length. I also looked at the
> "genomic Feature" to add gene length but this also relies on UCSC browser.
>
> Kindly guide me to analyse RNA seq data for Arabidopsis genome.
>
> Waiting in anticipation,
> Regards,
> Divya Vashisht
>
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