Hello Everyone, I am using DESeq2 for DEG analysis. I have a total of 8 samples( 1 duplicate for each condition so 4 different conditions) At this point of the analysis:

resultsNames(dds)
resLFC <- lfcShrink(dds, coef=4, res=res, type="apeglm")

I know that this part is used for shinking the lof2 fold change value to reduce the non-significant values but it’s not clear to me why by default is 2? with 2 I get error like 'coef' should specify same coefficient as in results 'res'

But in res I have this

res <- results(dds, alpha = 0.01)

it’ words ok if I set coef=4 but I’d like to understand why and in particular if it's correct 4

Thank you

Take a look at the section of the vignette that talks about the results() function. Without arguments it picks the last coefficient.