Thanks to PVCA I finally found a tool to check the effect of all my suspected confounders I annotated in my proteome project.
But now my problem is that I don't really know what to correct for and what to better leave.
First, should I now remove all major effects (eg data.processed, amountOfCells, Gender, Age) ?
Do I need to take special care of the covariates (eg: sample-origin:age.in.years?
Which package would you recommend to use for correction?
Thanks a lot!