[BioC] Using edgeR with no replicates, estimating dispersion and the pseudo.alt slot

WATSON Mick mick.watson at roslin.ed.ac.uk
Thu Oct 25 17:37:48 CEST 2012


We have a collaborator with RNA-Seq data with no replicates - and yes, I understand the limitations of this.

In the egdeR manual, one solution suggested to estimating common dispersion is choosing a value based on experience e.g. "d$common.dispersion <- 0.4".  However, this has the disadvantage of not filling up the pseudo.alt slot of the object, which are useful measures of normalised expression.  The estimateTagWiseDisp() function then fails.

It's fairly trivial to edit the estimateCommonDisp() function to accept a user provided common dispersion value, but I am not sure this is entirely valid.

The question being how to populate the pseudo.alt slot when you are estimating the common dispersion parameter yourself, and whether it is even valid to do so.


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