Question

Generate Heatmap after DEseq2 analysis

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7.5 years ago

nicolas.hipp ▴ 10

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 • 4.1k views

ADD COMMENT • link updated 7.5 years ago by Nicolas Rosewick 11k • written 7.5 years ago by nicolas.hipp ▴ 10

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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

ADD REPLY • link 7.5 years ago by Farbod ★ 3.4k

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

ADD REPLY • link 7.5 years ago by nicolas.hipp ▴ 10

score 2 · Answer 1 · 2016-11-02

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7.5 years ago

Nicolas Rosewick 11k

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

ADD COMMENT • link 7.5 years ago by Nicolas Rosewick 11k

score 0 · Answer 2 · 2016-11-02

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7.5 years ago

Ron ★ 1.2k

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

ADD COMMENT • link 7.5 years ago by Ron ★ 1.2k