Dear all,

I'm doing an EdgeR analysis and made some GOF plots after estimating
geneewise dispersion and fiting my data. I noticed that my values in the
first half of my plot are consistently a bit lower then theorethically
expected under the chisquared distribution. I'm trying to understand how
this comes. I guess it has something to do with underestimating the
variance because of the squeezing of the genewise dispersion towards the
trended dispersion? But why underestimating and why at the lower variances?
I don't see this in the gof plots in the authors paper ([McCarthy
2012][1]). And does this have some implications on my analysis?  I've put a
url to the gof plot and the BCV plotbelow.

Somebody cares to shed some light on this matter for this statistical
genomics novice? :)

Best regards

GOF plot:
 http://s16.postimg.org/dtldp2o85/Rplot.png<http://s16.postimg.org/dtldp2o85/Rplot.png>
BCV plot:
 http://s29.postimg.org/qnzg7e0w7/Rplot01.png

  [1]:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3378882&tool=pmcentrez&rendertype=abstract

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