I'm a newbie in R and I am trying to use DEP for the first time and I have a couple of questions:
1) I was wondering if it is possible to use DEP with an output from MaxQuant. I know the workflow for TMT analysis requires the output from IsobarQuan, but I imagined that if I can get the same columns in my MQ output it could work. If yes, what columns would I need to change/add?
2) I'm trying to follow the "Introduction to DEP" code, but I am getting stuck in the make_unique function.
data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")
I don't get any error in return and I do have those two columns (Gene.names and Protein.IDs) in my 'data' dataframe, however I am not getting the new 'name' column that is supposed to be generated in that function.
3) I have two treatments and a control condition in my dataset. Can DEP handle it? Or does it has to be max 2 conditions (control and treated)?