DESEQ2 control vs multiple treatment

Question

[bioinfonerd]

Hi I have four arms of a study with 50 matched patient samples data for all Arms 1,2,3 and 4 where

Arm1: Control
Arm2: Drug1
Arm3: Drug2
Arm4: Drug3

How can I compare Arm2,3 and 4 with Arm1 individually performing a DESeq. Could you please help me with the DESeq design? Thanks!

Answer 1

[Martombo]

you can specify the samples to test in the function results()

results(dds, contrast = c("condition", "Drug1", "Control"))

"condition" here is the name of the factor in your colData object. Once you have the individual results for each drug you can compare the log2FC you get and the number of significant DEGs and so on...

[bioinfonerd]

Thanks a lot! It works