Hi, Just to add to Ulrich's message: Xpress and ASAPratio values also are not parsed into iProphet.pep.xml and in general it seems that the current viewer not fully adjusted for iProphet output (or maybe the other way around). Like Ulrich, I'm also using iProphet to combine results from different search engines - in the current pepXML output there are 2 probabilities pepP (which seems like the highest PP probability found for duplicated peptides) and iP (which I assume is the one to follow), but I can't see the sensitivity and error curves of either of them and "more_pepanal.pl" output is just a single line with the location of the iProphet.pep.xml file. I also wonder which of one of the probabilities is used and reported by the "Calculate Statistics" option. I'm using TPP v4.3 JETSTREAM (unstable dev prerelease) rev 0, Build 200903041031 on Mac with OS 10.5.6 but saw similar output on RPP v4.2 on PC with winXP. Thanks, Oded
On Mar 20, 7:50 pm, Ulrich auf dem Keller <ukel...@interchange.ubc.ca> wrote: > Hi Natalie and David, > > I am using iProphet to combine results from different search engines > on the same experiment. It works very well and enhances the number of > reliable identifications significantly. Thanks for this piece of > software! > > A minor drawback at the moment is that libra quantification values in > iProphet pep.xml files are not .parsed by PepXMLViewer. It would be > great if you had time to integrate this option in future releases. > > Thanks a lot. > > Cheers, > > Ulrich > > On Mar 10, 2009, at 10:06 AM, Alex_PCB wrote: > > > > > Hi all, > > I'm re-posting a question on iPROPHET. > > > Here we go: > > > I am trying to run iPROPHET within the latest version of TPP (4.2) > > and got a little confused with the pipeline. I will try to elaborate > > a > > few questions and would appreciate any help. > > 1) I 've been using TPP for a few months now and my understanding is > > that I should run iProphet in the xinteract command (something like - > > ip). However, i don't quite understand which models i should use. For > > example, i have three technical replicates of a MUDPIT experiments > > with 20 fractions per replicate. Should I call all my tandem pepxml > > files from the three experiments within the same xinteract, > > right?!?!?! Should I enable all models??? > > 2) There is a -E option to label spectra. How should I use that? > > 3) What if I want to combine different database search results? Is > > the > > procedure similar? I mean, should i use the same models? > > 4) One more thing, my experiments are iTRAQ labeled. How iProphet > > would deal with it? > > Thank you for your time. > > regards, > > Alex --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
