DESeq2 genes which vary between 4 groups

Question

[j.obrien2013]

I am trying to identify which genes are significantly variable in four groups. How I was doing this was through:

Samples_results<- results(Samples_dds, alpha = 0.05, lfcThreshold = 1)

Which then provided me a list of a few hundred genes which were over the threshold. However, I am not sure if this was the correct way of testing this, and I was wondering if anyone had any advice?

Thanks!

Answer 1

[Kevin Blighe]

It sounds like you want to do a likelihood ratio test in order to capture genes whose variances differ across your four groups. If this is the case, then you will likely want to perform, for example:

dds <- DESeqDataSetFromMatrix(..., design= ~ group)
dds <- DESeq(dds, test = 'LRT', reduced = ~1)
res <- results(dds)

Please take a look at the 'likelihood ratio test' section of the vignette.

Kevin