DESeq2 and GLM with grouped samples in two conditions

[friducha]

Hi all,

I came across this post from Simon Anders, suggesting to use a GLM if one has grouped samples across the conditions.

Your data is not grouped, is it? If, say, samples CD90.1, UtESC-.1, and UtESC+.1 are from one mouse, CD90.2, UtESC-.2 and UtESC+.2 from a second mouse etc., a GLM will give you a lot of extra power.

I have a cell line RNAseq experiment with two conditions, WT and DISEASE, and within each group I have two individuals x two independent clones, so the final design looks like this:

WT Group: INDIV1-CloneA, INDIV1-CloneB, INDIV2-CloneA, INDIV2-CloneB

DISEASE Group: INDIV3-CloneA, INDIV3-CloneB, INDIV4-CloneA, INDIV4-CloneB



How can I change the parameters on DESeq2 to use a GLM as Simon suggests for this type of design?

[dpryan]

You'd use a design like ~INDIV+Group, where "INDIV" is 1-4 (as factors!) and "Group" is "WT" and "Disease". This assumes that there's no interaction, which you could also add in if needed.