[spctools-discuss] QualScore - 0 dtas written

Dear all, I am very interesting on using QualScore. I managed to get it running within the TPP GUI but I believe there's a problem with the output. It seems the tool detects the unassigned spectra but none is then written in the output. The qdir.coef file contains only NaN values. I am inclu

[spctools-discuss] QualScore input format

Hello, I have downloaded the QualScore tool from this sourceforge and I would like to use it to score some spectra. The man show this: Usage: java -jar qualscore.jar but I don't know what the is. Where can I find the struct

Re: [spctools-discuss] QualScore cannot be found anywhere:(

Hello Flora, The QualScore code can be found on our open online repository at: https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/qualscore/ That being said, we have not updated it in some time, and have heard reports that it might not be compatible with recent versions of Java. It is on our

[spctools-discuss] QualScore cannot be found anywhere:(

Recently I was trying to assess the quality of unassigned spectra in MS/MS experiment and I came across this nice paper which is the base of QualScore Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-

Re: [spctools-discuss] qualscore mzXML parse error

I'm getting a very similar error. Has anyone been able to resolve this yet? > java -jar C:\TPP\bin\qualscore.jar -c 1.0 -p 0.1 .\interact.iproph.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 warr

Re: [spctools-discuss] qualscore mzXML parse error

Huh, that is odd. The actual number of spectrum_query elements in the file is 9721. Is there any filtering that could explain the one that doesn't end up in the final tally? There's nothing funny about the pep.xml file -- it came out of a standard TPP 4.7.1 workflow. Also, when I try this on a

Re: [spctools-discuss] qualscore mzXML parse error

Hi Damon, I wonder if this has something to do with this index mismatch: XML Loading interact data: 1000 2000 3000 4000 5000 6000 7000 8000 9000 9721 Interact data file contains 9720 entries. I am not sure why but notice that the entries are off by one. Perhaps that is a clue to the

[spctools-discuss] qualscore mzXML parse error

I'd like to use qualscore from the command line on some pepXML and mzXML files, but I'm running into an mzXML-parsing problem. Full output of qualscore when run on my interact.pep.xml file is pasted below. The mzML file in question was converted from a QE raw file using msConvert 3.0.9576 with

Re: [spctools-discuss] QualScore question

Thank you David for your quick reply and consideration. I have similar .coef file with "NaN"s. I hope it is an easy fix and will wait for the working version. In the meantime, is there any other method in TPP to help collect/salvage the unassigned spectra (regardless of their quality)? Regards,

Re: [spctools-discuss] QualScore question

Hello, I also managed to get qualscore running with similar results, specifically "0 dtas written..." on two different datasets. In my case both .coef files had values that were NaN "not a number" suggesting a problem in the qualscore calculations. I have to still track this bug down but it is po

[spctools-discuss] QualScore question

Hi, I have managed to get Qualscore run on my machine (PC, windows 7) and here is the tail of what I see when the Qualscore finished: Features calculated for: 26701 (256137ms) Training set: 9721/12890 (good/bad) Unassigned spectra: 13703 Quality score calculation time: 171 ms Writing classifier

[spctools-discuss] Qualscore - 0 spectra written/NaN coefficients

Dear all, I'm trying to run qualscore to retrieve any non-matching spectra for re-matching against additional RNASeq-derived protein databases, however qualscore doesn't output any spectra (and returns NaN coefficients) even though it mentions there are unassigned spectra (15194) after the init

[spctools-discuss] qualscore

I am trying to evaluate data by qualscore and run into some problems. When I run qualscore on a peptide prophet pep.xml file derived from a mascot search it fails to identify any valid high quality spectra and classifies all spectra as bad. Peptide prophet does however report the expected number

[spctools-discuss] qualscore error message

Dear all, I realize that there has been people post this problem before, but I just don't know whether my problem is related to the newest version of TPP and JRE, so I decide to make a new post. My apology if this is redundant. version of TPP:4.6.2, JAVA: Jre7 in win7 x64 EXECUTING: run_in c:

[spctools-discuss] Qualscore error

Hi TPP community! I'm trying to run Qualscore on some data I have recently acquired. I've had no problems so far, except, when I run Qualscore on my pep.xml data, I get the following error. Could someone shine some light on this??? Thanks! Alex Command 1 [Thu Jul 5 12:20:13 2012] [ Sh

Re: [spctools-discuss] Qualscore

Hi, Does somebody has extensive experience with the qualscore tool and possibly knows a solution to the problem mentioned below? Many thanks in advance, Gerben On Sep 28, 2010, at 12:41 , Gerben Menschaert wrote: > Hi all, > > By including the extra classes, the qualscore is working now. > > S

Re: [spctools-discuss] Qualscore

Hi all, By including the extra classes, the qualscore is working now. Still I encounter another problem. My workflow: MS/MS identification with Mascot server results in a *.dat file. Conversion of the *.dat file to a *.pep.xml file (using the TPP pipeline). Analyse peptides using xInteract to

Re: [spctools-discuss] Qualscore

Everything you need to run qualscore should be here: http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/qualscore/lib/ -David On Fri, Sep 24, 2010 at 12:08 PM, Vishal Swaroop wrote: > It is also important to know which version of JFreechart is used by > qualscore. > Quick view of qualscore

Re: [spctools-discuss] Qualscore

It is also important to know which version of JFreechart is used by qualscore. Quick view of qualscore main class shows import of "org.jfree.data.SeriesDataset' which I was able to find in "jfreechart-0.9.19" but other import (org.jfree.chart.Marker) was not available. When I tried latest version

Re: [spctools-discuss] Qualscore

Hi Gerben, I realized that you are missing *jfreechart* jar in classpath, is it not included with TPP_Setup_v4_4 , check if it is available under c:\Inetpb\tpp-bin if not then then you can try downloading it and set it in classpath. Thanks On Fri, Sep 24, 2010 at 9:20 AM, Gerben Mensch

Re: [spctools-discuss] Qualscore

Hi Gerben, Though I am not using it, but as per error it looks like application is not able to find "qualscore.jar" Are you running from this from command prompt ? Before running the command set this in command window and then try set CLASSPATH=%CLASSPATH%;c:\Inetpub\tpp-bin\qualscore.jar Th

[spctools-discuss] Qualscore

Dear all, Is anybody using the QualScore module within the TPP? Is it still in use? Running it gave me the following error: run_in c:/Inetpub/wwwroot/ISB/data; java -jar c:\Inetpub\tpp-bin \qualscore.jar -c 1.0 -p 0.1 F026703.pep.xml

[spctools-discuss] Qualscore Arrayindexoutofbounds exception

Hi everyone, I have been trying qualscore 1.0.2, but having quite a few problems getting it to work properly. I followed Frank Posthast's suggestion to include -Xms750m to solve the outofmemory issue, and it worked. The error msg for the latest problem that I encountered is as follows: [Thu Jun

[spctools-discuss] Qualscore

Hi all, I was able to run ProbID and TPP!! Now I'm trying to use QUALSCORE. But I get this error: [EMAIL PROTECTED]:~/Desktop/qualscore$ java -jar qualscore.v1.0_2.jar interact.pep.xml QualScore version 1.0_2 Copyright (C) 2006 Institute for Systems Biology, Seattle WA QualScore is free software