Hi!
I am quite new to proteomics and I have one technical question.
I have analysed the proteomics of some cell lines with TMT and I have received the results in Proteome Discoverer. Each cell line was analysed in triplicate. I have not made the calculations myself and I only received the results file. The file contains some of the comparisons I want (for example, metastasis vs primary) but I would like to make other comparisons.
I am looking for an R package that allows me to do that and I am interested in DEqMS.
My question is: what kind of input data should I use? Normalised abundances or scaled abundances?
Thank you!
Best wishes,
Maria