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.
