Hi,
I now want to calculate the FDR of search result which has been
processed by PeptideProphet.
I tried probability (the column named probability), but the result is
weird.
Then I tried fval and found the number of PSMs (FDR <= 0.01) is very
close to that produced by expect in X!Tandem or lnEvalue in MSGF+.
But when I combined the two search results ( X!Tandem and MSGF+ ) using
InterProphet and calculate the FDR using fval, the number of PSMs is far
less than that derived from single search engine.
How this happen? Can anyone explain me this ? And whether the fval
value can be used to calculate FDR?
Thanks!
Best
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