[BioC] heatmap with variance stabilizing transformed expression data in DESeq

[Steve Lianoglou]

Hi Li,

On Wed, May 8, 2013 at 12:32 PM, Wang, Li <li.wang at ttu.edu> wrote:
> Dear Steve
>
> Thank you for your suggestion!
> The four FC data is output from edgeR, which I used for the differential expression analysis.
>
> I will try to load the entire data set, to do the transformation in DESeq2.

Note that edgeR also has its own suggested ways to do similar things,
as mentioned in Section 2.10 of the edgeRUsersGuide ("Clustering,
heatmaps, etc"). Might be helpful to look at those along with the
cited case studies that appear latter in the guide since you are
already in edgeR-land for your analysis.

I think the right way to do this is still an open question so trying a
few different methods to see how they behave is probably a good idea.

HTH,
-steve

--
Steve Lianoglou
Computational Biologist
Department of Bioinformatics and Computational Biology
Genentech