[BioC] Error messege in edgeR: Error in t(y) + prior.count.scaled : non-conformable arrays

[Steve Lianoglou]

Hi,

On Wed, Feb 5, 2014 at 7:23 AM, Navonil De Sarkar <navonil.de at gmail.com> wrote:
> I am analyzing paired samples (RNA-seq). I am facing problem with edgeR at
> y <- estimateGLMTrendedDisp(d, design) step where it is saying error
> message "Error in t(y) + prior.count.scaled : non-conformable arrays"
>
> although it was ok with the step y <- estimateGLMCommonDisp(d, design)
>
> Apparently in the assignment step something is happening [design <-
> model.matrix (~Patient+Tissue)] and when I am trying to see whats there in
> store at Design, its showing the matrix leaving the one of the sample
> column absent.

Could you be more specific? If your design matrix isn't too big,
perhaps you can show it, as well as the levels of Patient and Tissue.

My guess is that the sample that looks to be "absent" is likely just
absorbed as the (Intercept).

-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech