[BioC] time series data edgeR?

Ryan rct at thompsonclan.org
Mon Dec 16 17:57:42 CET 2013

Yes, edgeR can handle this case. You have a couple of options. The 
conceptually simplest one is to treat the timepoint as a second factor 
and fit a two-factor additive model (i.e. model.matrix(~genotype + 
timepoint) ). Another option is to use natural splines. This is an 
approach that I am not personally experienced with, but it has been 
discussed before on this list, so you should be able to find an example 
in the archives. Personally, I would recommend using the two-factor 
analysis initially, and only switching to something more complex if you 
decide you need it.

On Mon Dec 16 08:44:50 2013, Jahn Davik [guest] wrote:
> I have RNA seq data from two genotypes over five time points and I have been looking for software that handles such situations. I hoped edgeR would provide me with the the tool and that the edgeR Users Guide would contain coded examples. Alas, I cannot find anything on time series there.  Has anyone addressed 'my' situation? If so, I would appreciate being notified.
> best regards
> jahn
>   -- output of sessionInfo():
> NA
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