I am conducting gene expression analysis for a time course experiment. I have six time points. At each time point three replicate RNA data were collected. Samples within and between each time point are independent. I am interested in checking the expression profiles of genes so that I can group them. Specifically I am interested in conducting the following orthogonal contrasts

T1 vs T2

1/2 (T1+T2) = T3

1/3 (T1 + T2 + T3) = T4

1/4 (T1 + T2 + T3 +T4) = T5

How would I implement this contrasts in DESeq2.

hi,

Can you phrase your question with respect to the information in ?results. We describe there how to formulate contrasts like you are interested in, but if you need more information which is missing, let me know.