Luis, I finally got my PepXMLViewer working. I opened the file, and there is no entries with exact zero probability. But there are tons of entries with ~0.05 probability. Does that matter? Or QualScore only considers that zero probability as bad spectra?
The data is LTQ data, and first is searched under X!tandem. The result I used is from TPP. Thanks again! Ping On Apr 15, 3:42 pm, Luis Mendoza <lmend...@systemsbiology.org> wrote: > 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/... > > 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 <yanpp...@gmail.com> 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 <lmend...@systemsbiology.org> 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 <yanpp...@gmail.com> 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 spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
