Help understanding contrasts differential expression

[Klorator]

Hi,

I'm trying to cobble together a script performing differential expression with DEqMS and am getting different output from my script compared to using Amica. Why am I getting one output (one column of p-values) from my script but an output for every comparison from Amica?

I've followed the vignette, point 2.2, and the code runs. My question for now revolves around the contrast. I've used a character vector cont <- c("A-B", "A-C", "B-C") as seen in the limma::makeContrasts documentation. This later outputs one dataframe/column of p-values for everything. On the other hand, when my colleague uses Amica they get a dataframe for every comparison (in this case three).

Can you help me understand how Amica (and thereby limma/DEqMS) uses the contrasts and what the difference would be caused by in this case?