Dear Hannes, thank you for your reply. By "filter," I assume you mean the "maximum valid expectation value" in the output and refine settings of X!Tandem? If so, I've performed the following experiment.
Evalue 1e-2: 8 decoys / 24280 non-decoys Evalue 1e-1: 105 decoys / 31902 non-decoys Evalue 1e0: 793 decoys / 38363 non-decoys Evalue 1e1: 3197 decoys / 42706 non-decoys Evalue 1e2: 4642 decoys / 44256 non-decoys Thank you for your advice -- I will attempt to build the Pos and Neg distributions using the more liberal cutoffs. My goal is to obtain a SpectraST library to interrogate SWATH datasets, using OpenSWATH, of course! What kind of decoy to non-decoy ratio is satisfactory for FDR modelling, in your experience? Vadim On Apr 3, 2014, at 11:28 AM, Hannes Röst <[email protected]> wrote: > Hi Vadim > > This will most likely _not_ work. It would probably be better if you > do not filter before xinteract but give it the full X!Tandem output > and then filter afterwards based on the computed probabilities. This > way you also might increase the total number of retained hits at a > fixed FDR. > > Hannes -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
