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).
pg_matrix contains protein intensities which are calculated with MaxLFQ using normalised precursor intensities contained in the Precursor.Normalised column.
Hi Vadim,
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?
I'm a beginner in proteomics and also have limited experience with R.
Thank you very much for the excellent software.
Best regards,
Ko