DSeq2 : multiple treatments,developmental stages and genetic backgrounds
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 !
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mchimich •
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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.