[BioC] DEXSeq dispersion trend estimation?

Ryan C. Thompson rct at thompsonclan.org
Mon Mar 31 23:37:29 CEST 2014


I am trying to understand the methods used in DEXSeq, and I was hoping 
you could clear up some of the details of the dispersion trend squeezing 
strategy. In particular, when fitting the dispersion-mean trend, what is 
used as the mean for a given exon? Is this computed only based on the 
exon's own counts, or is it the mean of all the counts for that exon, 
including the sum of counts in other exons? If it is the latter, 
wouldn't the mean be identical for every exon in the same gene, since 
the total counts for that gene are constant, and if so, is this the 
intended effect?


-Ryan Thompson

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