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Generate Heatmap after DEseq2 analysis

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

rna-seq deseq2
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updated by Nicolas Rosewick Nicolas Rosewick • written by nicolas.hipp • nicolas.hipp

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

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written by Farbod Farbod

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

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written by nicolas.hipp • nicolas.hipp

2 answers

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

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written by Nicolas Rosewick Nicolas Rosewick

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

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written by Ron Ron

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