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 On 3 April 2014 20:19, Vadim Patsalo <[email protected]> wrote: > Dear TPP experts, > > I would like to run PeptideProphet and iProphet. > I use the following command: "xinteract -i -dDECOY -OAdtP -l6 -I1 -I5 -I6 > -I7 *xml" > > The pepXML contains X!Tandem search results, 22063 in total, only 8 of which > are DECOY matches (reversed sequences, {KR} remain in the same place). > The results were kept with the following expectation cutoffs: > > <note type="input" label="output, maximum valid expectation > value">0.01</note> > <note type="input" label="refine, maximum valid expectation > value">0.01</note> > > Given that there are only 8 decoys, can PeptideProphet and iProphet succeed > in creating an accurate discriminant function? > > Thank you in advance! > Vadim > > -- > 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. -- 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.
