The first warning is just a disclaimer that can be ignored especially when your data is validated with decoys. The second warning should really be an error since with the current PeptideProphet modelling of Myrimatch, Inspect, OMSSA, and Phenyx is done using semi-parametric model that *requires* you to have decoys in your database and search results.
-David On Sat, Jul 24, 2010 at 10:04 AM, Taejoon Kwon <[email protected]> wrote: > Hi, > > I am benchmarking several different search engine output, and would > like to evaluate 'standardized score' through TPP. Most of them > support pepxml format (hooray!) so I can feed them into TPP pipeline, > at least. But TPP says warning about the output as below (e.g. > Myrimatch): > > ---- > WARNING!! The discriminant function for Myrimatch 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. > WARNING: Myrimatch only support semi-parametric PeptideProphet > modelling, which relies on a DECOY search. > ---- > > I think that it is because each search engine reports different type > of score (at least different to Xcorr and deltaCn), so PeptideProphet > cannot use this as proper score function variables. And I believe that > another reason is that there is no 'score function' for each search > engine. > > How can I make these TPP output as 'publishable scientific results'? > Is there easy way to plug in the score function into code if I get > that by training with custom dataset? > > Thanks, > > Taejoon Kwon > > -- > 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.
