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

[Gordon K Smyth]

Kasper,

I hear you.  It's not so easy to achieve (because the function issuing the 
warning doesn't know which gene it is working on), but we'll have a think 
about it.

Best
Gordon

On Fri, 22 Jul 2011, Kasper Daniel Hansen wrote:

> 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
>

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