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). And does this have some implications on my analysis? I've put the gof plot and the BCV plot in attachment.
Somebody cares to shed some light on this matter for this statistical genomics novice? :)
Best regards
