[Bioc-sig-seq] edgeR Warning Messages from maximizeInterpolant called from estimateGLMTagwiseDisp

[Kasper Daniel Hansen]

On Fri, Jul 22, 2011 at 9:31 AM, Sean Ruddy <sruddy17 at gmail.com> wrote:
> Hi Gordon,
>
> Thanks for the reply. That's good to know I shouldn't be worried about the
> results, but then again I'm not really sure, as you say, if I should even go
> down this road. Using the standard edgeR normalization would also be
> meaningless in my case unfortunately. I have two data sets of counts each
> belonging to different organisms. One data set runs smoothly and the other
> has all these problems yet the experiments done on both were exactly the
> same. Kind of puzzling and unfortunate but I will investigate more into what
> you're saying about the offsets and see if I can't adjust my
> strategy. Thanks for the insights!

While I agree with Gordon that having warnings in a few genes are
hardly problematic, it would perhaps make sense to make it easy for
the user to identify exactly which genes (rows) have warnings
associated with them,  Having been bitten by convergence problems in
the past, I believe it is always prudent to check the data. Just a
suggestion, and I apoligize if this is already (easily) possible.

Kasper