[BioC] RNA seq analysis of Arabidopsis genome

[Wolfgang Huber]

Dear Matt

would it be a feasible alternative for Divya to use expression level 
(estimated e.g. by each gene's average count in the data, or some 
function thereof) for sampling bias adjustment in bias.data, rather than 
length?

	Best wishes
	Wolfgang


Sep/19/11 2:34 PM, Matthew Young scripsit::
> 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 at 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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>>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber