Hi, Luis, Thanks a lot for the response.
I run the PeptideProphet on x!Tandem results. And then I run the Qualscore on this all.pep.xml file, and use the -p0 option, but I got following message: java -jar qualscore.v1.0_2.jar ../../temp/ all.pep.xml QualScore version 1.0_2 Copyright (C) 2006 Institute for Systems Biology, Seattle WA QualScore is free software and comes with absolutely no warranty. XML Loading interact data: 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 11000 12000 13000 14000 15000 16000 17000 18000 19000 20000 20124 Interact data file contains 20123 entries. 695 +1 were removed. Enumerating scans: processing FHCRC_yeast_600ng_02.mzXML... 500 1000 1500 2000 2500 3000 3500 4000 4500 5000 5500 6000 processing FHCRC_yeast_600ng_01.mzXML... 6500 7000 7500 8000 8500 9000 9500 10000 10500 11000 11500 12000 12500 processing FHCRC_yeast_600ng_03.mzXML... 13000 13500 14000 14500 15000 15500 16000 16500 17000 17500 18000 18500 19000 19302 Features calculated for: 19302 (996935 ms) Training set: 10054/0 (good/bad) Unassigned spectra: 1469 ERROR: Training set distribution unusable. Do you have any suggestion for it? I search for the same topic in the group. Someone said it might because of the mzXML files? 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 -~----------~----~----~----~------~----~------~--~---
