Hi Ping, By "the same results", do you mean that all of the program output is identical? (e.g. the number of spectra used, etc) Or just that you also get an unusable training set? I would first make sure that you are setting the -p0 option successfully by opening the PeptideProphet results in the PepXML Viewer, and look for entries with zero probability; there should be many. You can also look at the following thread for some other hints: http://groups.google.com/group/spctools-discuss/browse_thread/thread/a50fe1c74e52cc91/d736d07e295d0ca2?lnk=gst&q=qualscore+features#d736d07e295d0ca2
Otherwise the software does suggest that it cannot find any "bad" spectra to derive a training set. What kind of instrument did you use to acquire your data? Did you do any pre-processing before searching? --Luis On Wed, Apr 15, 2009 at 1:43 PM, Ping <[email protected]> wrote: > > Hi Luis, > > Thanks a lot for your response. > > I used the x!Tandem results, all.pep.xml + original mzXML files as > input. But I got following error. > > Features calculated for: 24780 (1171916 ms) > Training set: 12699/0 (good/bad) > Unassigned spectra: 2611 > ERROR: Training set distribution unusable. > > I searched the post in the group, and used -p0 option, but still I got > the same results. Does that mean my original mzXML has too little low > quality spectral data? > > Thanks again, > > Ping > > On Apr 15, 11:44 am, Luis Mendoza <[email protected]> wrote: > > Hello Ping, > > Qualscore uses a pepXML file with *all* PeptideProphet probabilities > (i.e. > > P>=0.0). As such, you will first need to search your data and run it > > through PeptideProphet before you can use QualScore. You can find more > > information about the algorithm in the publication listed in the README > > file: > http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/qualscore/REA... > > > > Best of luck, and thanks for trying out our software. > > --Luis > > > > On Wed, Apr 15, 2009 at 10:15 AM, Ping <[email protected]> wrote: > > > > > Hi All, > > > > > I just downloaded the qualscore from sashimi, and installed it on my > > > Ubuntu machine. The command line should be: > > > > > java -jar qualscore_v1.0_2.jar someXML file > > > > > I am not sure what this XML suppose to be look like? Can anyone send > > > me an example of it? > > > > > I am a newbie in this area. So please forgive me if the question is > > > too simple. > > > > > Thanks! > > > > > Ping > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
