How can I create a heatmap from DEG analysis of three treatment groups?

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1

Hello,

I am following this tutorial for DEG analysis of my RNAseq data. However, my data has one factor with three different levels.

How can I create a heatmap including all the DEGs from the pairwise comparisons that DESeq2 has outputted? I have three DESeq2 results files (one for each pairwise comparison between my three groups).

Thanks!

2

Welcome @assignmentlodge

The usual way is to plot each pairwise result individually. You’ll see this in some publications.

For something more interesting, maybe try the other DE tools such as Limma – you can set one factor level as the contrast to see the effect on the other two conditions (factor levels), all together one set of visualization graphs. Using the control condition as the contrast is one place to start.

You can use the Featurecount result files you have now but should combine them into a matrix. We had another question answered earlier today that has all the links. See → generate a common AnnotateMyID file from two different runs

Hope this helps! :slight_smile: