Hello everyone,

I was hoping to get some input on a problem I've been stuck on. Working on proteomics, I have two datasets from the same samples, one is the original dataset (og), and the other one accounts for PTMs (mod). Within them there are four different samples, young control, young treated, old control, old treated. I would like to find out what are the DEGs between

(young.treated.mod - young.control.mod)-(young.treated.og - young.control.og) and (old.treated.mod - old.control.mod) - (old.treated.og - old.control.og)

This is what I have so far

Age<-  c(rep('young', 'old', 'young', 'old', each =12))
Treatment <- c(rep('control', 'treated', 'shcontrol', 'treated','control', 'treated', 'shcontrol', 'shtreated', each=6))
Dataset<- c(rep('og', 'mod', each = 24))
exp_design<- cbind(Age, Treatment,Dataset)
exp_design<- as.data.frame(exp_design)

design <- model.matrix(~Treatment*Dataset)
fit <- lmFit(df, design)

`

However, this fails to inculde all of my desired variables I want to account for. A little bit stuck on how to proceed, so any input would be greatly appreciated!

Many many thanks Maria