[BioC] edgeR warning message when running Trended Dispersion

[Natasha Sahgal]

Hi Steve,

Thanks your reply. The information you asked for is below:

> dim(y2.filt$counts)
[1] 4514    6

> dim(design2)
[1] 6 3

Many Thanks,
Natasha

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-----Original Message-----
From: mailinglist.honeypot at gmail.com [mailto:mailinglist.honeypot at gmail.com] On Behalf Of Steve Lianoglou
Sent: 16 May 2013 14:18
To: Natasha Sahgal
Cc: Gordon K Smyth; Bioconductor mailing list
Subject: Re: [BioC] edgeR warning message when running Trended Dispersion

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