How are multiple conditions/comparisons done in v1.16 using lfcShrink?  Using the example from the package, eg.

cnts <- matrix(rnbinom(n=1500, mu=100, size=1/0.5), ncol=15)
cond <- factor(rep(1:3, each=5))

# object construction
dds <- DESeqDataSetFromMatrix(cnts, DataFrame(cond), ~ cond)

# standard analysis
dds <- DESeq(dds)
res <- results(dds)

# moderated log2 fold changes
resLFC_1 <- lfcShrink(dds, coef=2, res=res)
resLFC_2 <- lfcShrink(dds, coef=3, res=res)

The raw/adj p-values are the same, what's the correct way?

Thanks!

lfcShrink() only shrinks the estimated effect size (the log2 fold change) it doesn’t alter the p-values in the table. So you would need to run results() first on the respective coefficient. In version 1.18, I made it cleaner, such that you don’t have to provide ‘res’, it’s calculated internally for you.