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Hello,
I don't know how to calculate "relative" isoform abundance (proportions) for each gene from the eXpress output. One (naive) way to do that is to divide each isoform count by sum of all isoform counts for that specific gene, right?
But I think this may be faulty, since it's mentioned in the Online Methods of the eXpress paper that:
Lemma 14 in the supplementary material of the Cufflinks paper explains how to recover the abundances ρ_t from the parameters τ_t.
Looking at Lemma 14 of the Cufflikns paper and equation (6) in Online Methods of the eXpress paper, it looks like I need the estimated values for the parameter τ_t|l and w_p|(t,l) to do so. However, I don't know how to extract the values for these parameters from the eXpress output. I was wondering whether you could give me some comments and help please.
Thanks a lot,
Golsheed
I don't know how to calculate "relative" isoform abundance (proportions) for each gene from the eXpress output. One (naive) way to do that is to divide each isoform count by sum of all isoform counts for that specific gene, right?
But I think this may be faulty, since it's mentioned in the Online Methods of the eXpress paper that:
Lemma 14 in the supplementary material of the Cufflinks paper explains how to recover the abundances ρ_t from the parameters τ_t.
Looking at Lemma 14 of the Cufflikns paper and equation (6) in Online Methods of the eXpress paper, it looks like I need the estimated values for the parameter τ_t|l and w_p|(t,l) to do so. However, I don't know how to extract the values for these parameters from the eXpress output. I was wondering whether you could give me some comments and help please.
Thanks a lot,
Golsheed