DSeq2 : multiple treatments,developmental stages and genetic backgrounds

Question

[mchimich]

Dear users, I'm trying to upload a gene expression count matrix into DSeq2 but I'm still confused about how to create the different groups and replicates. My Table structure is as follow :

As you can see I did have multiple samples coming from different genetic background (wild vs mutant) different developmental stages (1d,2d,3d), and treatment (C,T) with 2 replicates (.1 and .2).

My question is how can I specify to DESeq2 this data structure starting from a count matrix table ?

Thanks in advance for your help !

[Devon Ryan]

Have you read the DESeq2 vignette and user guide? They give examples of this using a sample table, which is essentially what you're showing.