Hello,

I need to perform complex DESeq2 comparisons for mRNA sequencing data (I have biological replicates of each condition and subunit mentioned below).

I have two knock-down conditions (KD1 and KD2), and 1 scrambled RNA control condition (SCR). Within each condition, I have 4 subunits (1, 2, 3, 4) that each need to be compared to their corresponding whole-cell data (WC).

1. Compare each subunit to its corresponding whole-cell within the condition.
2. Use this data to compare across conditions (ex. KD1 subunit1_vs_WC compared against SCR subunit1_vs_WC).

Could someone provide more insight into how I could use the data from 1. to perform the comparisons in 2. ? I've already performed 1.

Thank you for your support.

Assuming that WC in your equation #2 is different in KD1 subunit1_vs_WC and SCR subunit1_vs_WC, this is just an interaction, and the easiest way to do that is to fit a cell means model and make the contrasts directly. There is a bit about this in the DESeq2 vignette, and it is explored in more depth in the limma User's Guide in section 9.5.2