TMT analysis

[dparrine]

Hey!

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? SO far I tried the following columns but it doesn't seem to work (see test_diff returns p-values in wrong order #2 comment):

 [1] "Protein.IDs"     "Protein.names"   "Gene.names"     
 [4] "FC_126C"         "FC_128C"         "FC_129C"        
 [7] "FC_127B"         "FC_128B"         "FC_130B"        
[10] "PSM"             "Unique.peptides"

2. I'm trying to follow the "Introduction to DEP" code for TMT and I get the following error when using the function 'TMT':

Error in make.unique(ifelse(name == "" | is.na(name), ID, name)) :
'names' must be a character vector

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)?

Thank you,

Debs