[BioC] Heatmaps for EdgeR

Steve Lianoglou lianoglou.steve at gene.com
Fri Mar 21 18:48:33 CET 2014

Hi Eleanor,

On Thu, Mar 20, 2014 at 4:36 PM, Eleanor Su <eleanorjinsu at gmail.com> wrote:
> Hi there,
> I'm an amateur edgeR user, and I'm having trouble generating a heat map for
> the differentially expressed genes. All examples that I've looked at
> requires that I normalize the counts but I've already normalized them prior
> to doing analysis in R.

Can you explain what you mean with that a bit more. You shouldn't be
doing any normalization of your actual counts prior to feeding them to
edgeR, are you?

> I'm running a glm with blocking and have generated
> my topTags. From here, I'm not sure how to generate a heatmap. Could you
> offer any advice or suggestions?

Look at section 2.10 of the edgeR User's Guide (Clustering, heatmaps,
etc.) where the authors identify this to still be a matter of
research, but they suggest to use "moderated log-counts-per-million"


Steve Lianoglou
Computational Biologist

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