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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Questions about the main report #855

Open Kokoushin opened 10 months ago

Kokoushin commented 10 months ago

Hi Vadim,

  1. I usually use the iq or diann R package to process the main report.

process_long_format("df.tsv", output_filename = "iq.tsv",annotation_col = c("Protein.Names", "Genes"), filter_double_less = c("Lib.Q.Value" = "0.01", "Lib.PG.Q.Value" = "0.01"))

Is there any way to directly convert the main report into the pg_matrix format?

  1. What is the relationship between the Precursor.Normalised in main report and the intensity in pg_matrix?

I'm a beginner in proteomics and also have limited experience with R.

Thank you very much for the excellent software.

Best regards,

Ko

vdemichev commented 9 months ago

Hi Ko,

  1. Yes, e.g. with diann_matrix function of the diann R package or any other custom script (it's several lines of R code to do this).
  2. pg_matrix contains protein intensities which are calculated with MaxLFQ using normalised precursor intensities contained in the Precursor.Normalised column.

Best, Vadim