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const-ae / proDA

Protein Differential Abundance for Label-Free Mass Spectrometry https://const-ae.github.io/proDA/
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import_MaxQuant filter #6

Open demar01 opened 3 years ago

demar01 commented 3 years ago

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 commented 3 years ago

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