[BioC] how to calculate gene length to be used in rpkm() in edgeR

[Ryan]

Hi Shirley,

The appropriate gene length to use is whatever gene length was used to 
compute RPKM values for data set B. If you don't have that information, 
then I don't see how you can compute comparable RPKM values for your 
data.

-Ryan

On Fri May  2 15:01:32 2014, shirley zhang wrote:
> Dear List,
>
> I've been used edgeR for differential expression analysis for data
> generated from the same tissue, but different conditions.
>
> Now I have a RNAseq data A (n=20), and would like to compare them with
> another RNAseq data B (n=1,000 across different tissues). Since data B is
> normalized and batch-effect adjusted RPKM value, I need to generate RPKM
> value for my own data A.
>
> I already had a count table, and would like to use rpkm() in edgeR, but
> first I have to get a gene length vector. My question is how to count gene
> length from an "Ensembl.gtf" file by taking into account the following:
>
> 1. Gene 1 is much longer than Gene 2 if including both exon and intron. But
>      Gene 1 only has 3 exons, and Gene 2 has 10 exons --> for the
> transcripts, Gene2>Gene1
>
> 2. For the same Gene, there are > 1 transcript isoforms.  In different
> tissues, different transcript isoforms will be expressed.
>
> Many thanks,
> Shirley
>
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>
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