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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