Question

How to combine replicates creating heatmap?

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alexandr.gopanenko ▴ 50

@alexandrgopanenko-11598

Last seen 16 months ago

Germany

Hello!

When I do DE analysis of my RNA-seq data I often have 3-4 replicates of each condition. So, I want present heatmap contaning only condition1_vs_condition_2.

I realize that it will not contain information about variations between replicates but I think it will be easy for understanding.

Thank you in advance,

Alexander Gopanenko

deseq2 edgeR heatmap.2 • 2.5k views

ADD COMMENT • link updated 8.1 years ago by Michael Love 43k • written 8.1 years ago by alexandr.gopanenko ▴ 50

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By replicates are these technical or biological replicates? I would never combine biological replicates in a heatmap, especially as you have only 2 conditions I can't see the point in that.

ADD REPLY • link 8.1 years ago chris86 ▴ 420

score 1 · Answer 1 · 2016-10-25

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Michael Love 43k

@mikelove

Last seen 3 days ago

United States

A heatmap is not a good way to show the differences between two numbers. Humans are not good at judging values by color. Plots showing spatial distances are much better.

Previous post on the topic:

A: DESeq heatmap based on threshold

ADD COMMENT • link 8.1 years ago Michael Love 43k

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Michael, thank you very much for your advice!

ADD REPLY • link 8.1 years ago alexandr.gopanenko ▴ 50