Hello,

I'm trying to figure out if there is a way to perform what I'm going to describe in DESEQ2. In the past, I used the workflow RNASeqGeneEdgeRQL to perform differential expression analysis. More specifically, in the paragraph 'Analysis of Deviance', it's described how to extend a comparison between two groups to three or more, in a specific experimental design.

Like in my previous post, let's assume it is:

Sample Variable1 Variable2

1 A x

2 A x

3 A x

4 A y

5 A y

6 A y

7 B x

8 B x

9 B x

10 B y

11 B y

12 B y

The aim is to identify genes which are DE among 3 or more groups (So, for istance, among the comparisons A.x-A.y , B.x-B.y and A.x-B.x). An output table is reported, showing logFoldChange and logCPM for each group, and single statistical values (p-value, FDR, F-statistic, in edgeR's case).

I'd like to perform an equivalent analysis in DESEQ2,

Thanks in advance for your help.

Can we continue on the previous thread instead?

Performing simple pairwise comparisons in DESEQ2