Thanks, David! For the second warning, does it mean that TPP cannot recognize decoy search results? I am using the following xinteract command now. Is there anything wrong?
/usr/local/tpp/bin/xinteract -Nmyrimatch.xinteract/ $SAMPLE_NAME.xinteract.xml -Op -dxf_ tmp/*.pepxml (Of course, *.pepxml have lots of decoy hits starting with 'xf_'. Taejoon On Jul 25, 12:36 pm, David Shteynberg <[email protected]> wrote: > 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 > > athttp://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.
