import_MaxQuant filter

[demar01]

Great method!

One question regarding the DEP before proDA. Shouldn't the argument filter = c("Reverse",
"Potential.contaminant") in the function import_MaxQuant be explicit before proDA?

How it would this affect the result?

[const-ae]

Hi Maria,

thank you for reaching out.
I am not sure if I correctly understand your question. I assume you talk about the DEP section in the Proteomics Data Import vignette. The DEP function import_MaxQuant() is defined as

import_MaxQuant(proteins, expdesign, filter = c("Reverse",
  "Potential.contaminant"), intensities = "LFQ", names = "Gene.names",
  ids = "Protein.IDs", delim = ";")

The filter that you suggest is already the default, so I don't need to explicitly specify it. However, I agree that for clarity I would be useful to include it in the vignette to avoid misunderstandings.

Best,
Constantin