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RNA-seq heatmap but compared to control rather than average expression

Sorry if this is a repeat, I couldn't find anything but please just redirect me if there is already posts about this

I have data from an RNA-seq experiment with a control condition and 10 other experimental conditions, with 3 replicates for each condition. I've been able to generate a heatmap using the Heatmap package in R and as I understand it underexpression/overexpression is shown compared to the average expression across all the samples. Is it possible to generate a heatmap where the changes in expression are shown in comparison to the control samples? And if this is possible how do you do it?

rna-seq heatmap r
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updated by jared.andrews07 jared.andrews07 • written by mar77 • mar77

1 answer

Sure, just plot the log fold change for each sample, remove the control samples, and don't scale by rows.

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written by jared.andrews07 jared.andrews07

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