[BioC] Limitations in edgeR?

[Steve Lianoglou]

Hi Eleanor,

On Tue, Apr 1, 2014 at 11:09 AM, Eleanor Su <eleanorjinsu at gmail.com> wrote:
> Hi All,
>
> I'm currently trying to analyze differential expression of piRNAs in some
> small data sets but am coming across issues that I didn't before when I
> analyzed with a larger data set. The larger data set contained 324 piRNA
> identities while the smaller data set contained half as many piRNA
> identities. Is there a minimum number of gene identities required in order
> to analyze differential expression in edgeR?

It's hard to help without knowing what the issues are that you are
running into, so ... what's going wrong?

One way you could explore this question yourself is to use the larger
(324 piRNA) dataset that "went well" and simply take half of the data
from it and rerun the same analysis on the smaller set. Do you get
different results?

While you're playing with that idea, please provide a follow up email
with more specific details about what the issues are that you are
running into with your new (smaller) dataset.

HTH,
-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech