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

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.