[BioC] edgeR questions

[Gordon K Smyth]

Dear Li,

Your study doesn't seem to present any difficulties for edgeR, and the 
analysis could be done as a whole.

If you would like more detailed advice, you would need to post the targets 
or samples table from your experiment showing the group membership of each 
sample, and a description of the questions you want to answer.

Best wishes
Gordon

> From: "Wang, Li" <li.wang at ttu.edu>
> To: Bioconductor mailing list <bioconductor at r-project.org>
> Subject: [BioC] edgeR questions
>
> Dear List Members
>
> My experimental design is set to contain two groups of RNA-seq and 
> within each group there are two subgroups(each subgroup with 8 
> replicates). Our goal is to identify differential expression genes 
> between two groups and also between two subgroups.
> I red through the case studies in edgeR user guide and has not found 
> such cases.
> How can we achieve the goals with edgeR?
> My current idea is to do the analysis between subgroups first and then 
> between groups. In the case, we can find the shared and different DE 
> genes.
> I donot know if we can do the analysis in one run.
> Any comments and suggestions are very much appreciated.
> Thanks in advance!
> Best wishes
> Li

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