[BioC] edgeR warning message when running Trended Dispersion

[Steve Lianoglou]

Hi Natasha,

On Thu, May 16, 2013 at 2:01 AM, Natasha Sahgal <nsahgal at well.ox.ac.uk> wrote:
> Dear Prof. Smyth,
>
> Thank you for your reply.
>
> Yes, I eventually did upgrade and realised that the warning message was no longer there.
>
> However, if I may ask a related question. I decided to try the same data below (but as an unpaired analysis) and got an error at the commonTagwiseDisp step. (Latest version of R).
>
> Code:
>> y2.filt = y[keep, ]
>> design2 = model.matrix(~group)
>
>> y2.filt = estimateCommonDisp(y2.filt, design2, verbose=T)
> #Disp = 0.60835 , BCV = 0.78
>
>> y2.filt = estimateTagwiseDisp(y2.filt,design2)
> #Error in prior.n/ntags * m0 : non-conformable arrays

What is the output of `dim(y2.filt$counts)` and `dim(design2)`?

-steve

--
Steve Lianoglou
Computational Biologist
Department of Bioinformatics and Computational Biology
Genentech