[BioC] DESeq /edgeR design problem for a small RNASeq

[Simon Anders]

Hi Eduardo

On 04/06/13 12:13, Eduardo Andrés León wrote:
> About ANOVA, I did some experiments with the edgeR anova-like test using
> the glmLRT function and the coef parameter.
>
> But as usual, both results were quite different.

Just to clarify: What you do with DESeq's GLM facilities is also ANOVA 
(or actually, both edgeR and DESeq do ANODEV, but this is just a 
technicality), and you should get roughly similar results. Are you sure 
you tested _for_the_interaction_ with edgeR?

> About the next step, the time course analysis, can this be done with
> DESeq, using the time as a new covariate (as with the drug) ?

In principle, yes. But now things get really complicated because you 
need to choose which time points to compare (as you have more than two).

   Simon