Hi,

I'm using DESeq2 for my analysis which is a time-series experiment. How do I fix my desire baseline instead of following DESeq's settings which chose one of the timepoints instead as the baseline? I'm assuming that it does so in order to generate a positive value?

Thank you.

Take a look at the vignette and the gene level workflow (linked from top of vignette). Both discuss the LFC and choice of reference level.