logFoldChange results in inverted comparison
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@b295d7f1
Last seen 19 months ago
Italy

Hi there!

I am using DEseq2 to perform different gene expression analysis. I was comparing in parallel

  • group A vs group B
  • group B vs group A

When I have compared the results of the two analysis, I have found that given a comparison A vs B nhe LogFoldChange value is not always equal to the inverse logFoldChange value of comparison B vs A. I was wondering if this is true because other factors are taken into account during the computation of LogFoldChange .

Best regards,

Giulia

#DESeq2 #LFC #RNAseq • 721 views
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Hi, this should not happen, could you show some examples and the code you ran to make the comparison ? Thanks

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ATpoint ★ 4.6k
@atpoint-13662
Last seen 11 hours ago
Germany

It is equivalent, only the sign changes. Be sure to have your code clean and organized so no leftovers of already used variables skew your comparison. Please provide a reproducible example in case you need further help.

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