[BioC] dispersion in edgeR
naomi at stat.psu.edu
Fri Jun 25 20:03:52 CEST 2010
I have 2 questions about dispersion in edgeR.
1) The model implies that as sequencing depth increases, the power
for testing differential expression comes to an asymptote. This seems odd.
2) Usually when using a shrinkage estimator, values of the original
estimates shrink monotonely towards the common estimate. So, if one
plots the moderated values against one another for 2 values of the
shrinkage parameter, the plot should be monotone increasing. The
plot was too big to attach, but what I did was:
I have not included my particular set of data, as I am pretty sure we
see this for any set.
This plot seems to imply that 2 genes could have the same moderated
dispersion values at prior.n=10 and very different values at
prior.n=30. This is not due to my
Naomi S. Altman 814-865-3791 (voice)
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348 (Statistics)
University Park, PA 16802-2111
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