Hi Robert, There is nothing that special about the OMSSA discriminant function that would make it unreliable. Since OMSSA requires decoys you can use these instead of the probabilities to compute the error rates and compare to those estimated by probabilities.
-David On Thu, Jun 30, 2011 at 12:34 PM, Robert <[email protected]> wrote: > Hi, > > since a while I process data from different machines with a pipeline > (find link attached), which first executes an OMSSA search against a > decoy database, and following validates the results with > PeptideProphet/ProteinProphet. The outcome looks quite reliable to me > (comparable to the Mascot hits) and is compatible with the PRIDE > converter. > > However, during the processing the following warning appears: > > "WARNING!! The discriminant function for OMSSA is not yet complete. > It is presented here to help facilitate trial and discussion. > Reliance on this code for publishable scientific results is not > recommended." > > So, may I publish the identifications or will there be an update > regarding the discriminant function? > > Best, Robert > > > http://groups.google.com/group/spctools-discuss/browse_thread/thread/f5f944d983ce9699/99c661635800bce2?lnk=gst&q=omssavalidation#99c661635800bce2 > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
