Hi, I want to find if one gene has a significantly different Log2FC than a different gene. (e.g. Gene A has LFC of 2.5, and gene B has a LFC of 2.8 - are they significantly different)

One way I'd thought of is to use the LFC and standard error calculated by DeSeq2 for each gene and calculate T test using this. Unfortunately I'm not sure if this is a reasonable approach. Any pointers would be great!

Thanks!

Hi Mike, Thanks for the reply. I hadn't really considered co-variance from the same gene family - that's a really good point. Say for example they're not from the same family, is my suggestion above reasonable?

If you need a test, when you take the difference between two estimates, their variances add. The SE^2 is an estimate of the variance, so you would expect estimate1 - estimate2 to have variance SE_1^2 + SE_2^2. Taking the square root gives a standard error for the difference.