Generate Heatmap after DEseq2 analysis

Question

[nicolas.hipp]

Hi everyone,

I have a problem to represent my RNAseq data. I have a list of DE genes as output of DEseq2. So I would like to make an heatmap of these genes across all my conditions (3 conditions, and 3 samples per condition)

Problems starts here because I don't really know which values I have to take in input of DEseq2. Can I sort my DE gene-list and perform my heatmap with the values provided by the rlog function of DEseq2?

Sorry for the naive question, maybe i'm totally wrong. Thanks

[Farbod]

Dear Nicolas, Hi

Please have a look at this Trinity page for "Automatically Partitioning Genes into Expression Clusters" and "Interactive analysis of DE features using MeV".

Maybe that could help.

~ Best

[nicolas.hipp]

Hello :) Thanks for the answer, I will have a look on it. Best ;)

Answer 1

[Nicolas Rosewick]

Read the DESeq2 vignette. There is a section regarding heatmaps using transformed data vsd or rld

Answer 2

[Ron]

You can take the expression values (FPKMS )of those genes in the samples and plot a heat map.