[BioC] DEXSeq dispersion trend estimation?
alejandro.reyes at embl.de
Tue Apr 1 07:16:23 CEST 2014
Thanks for your e-mail!
For all previous versions, the dispersion-mean trend was done using the
mean for a given exon. The latest version on the svn is including the
sum of counts from the other exons, but this is not optimal, since (as
you mention) the mean of the counts get inflated and each exon from the
same gene would have the same mean, for some cases, this causes the
dispersion-mean trend not to be obvious. We will change it soon in the
next commit of the svn, the reason we have not done it is because when
doing it we encounter some problems with the running times in subsequent
steps... my feeling is that it is a strange behavior of the GLM fitter,
and I already contacted the maintainer, so it is work in progress!
Will keep you updated,
> 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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