That's the issue I was thinking about, yes - so it sounds like using the "xinteract *.pep.xm" approach you're on to a new and different problem, then?
-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Bernt Sent: Thursday, July 02, 2009 10:15 AM To: spctools-discuss Subject: [spctools-discuss] Re: Does Peptideprophet accept only a limited no. of pepXML files? Hi Brian, Thanks for your response. I'm using TPPv4.2 Rev 1 on Windows XP. I read the thread on "limit on number of pep.xml files that can be analysed with interact" before, and Eric Deutsch was suggesting using <xinteract *.pep.xml> on the command line. I tried it, and it started processing all the 100 over files i had, but in the end there was a problem with the generated interact.pep.xml file. Were you going to suggest this <xinteract *.pep.xml> method? Bernt On Jul 1, 11:32 pm, "Brian Pratt" <[email protected]> wrote: > What operating system are you on (windows, linux etc)? My guess is that > it's probably about the length of the command line, rather than the file > count. We've had issues with this in the past, it might be borken again. > > Brian > > -----Original Message----- > From: [email protected] > > [mailto:[email protected]] On Behalf Of Bernt > Sent: Wednesday, July 01, 2009 3:14 AM > To: spctools-discuss > Subject: [spctools-discuss] Does Peptideprophet accept only a limited no. of > pepXML files? > > Dear all, > > I wonder if anyone has encountered this problem: For < 80 files, > Peptideprophet works normally, but when there are more than 80 files, > it doesn't start at all. > > If we split them up into 2 batches to run peptideprophet, the > statistical distributions that we obtain would be different since it > may happen that we unknowingly choose a group of poor scoring spectra > to model for 1 batch, while the other batch contains high scoring > ones. Would the peptideprophet probabilities obtained for the poor > scoring batch be reliable ? Ideally we should analyse the distribution > across all the files from a single sample (separated into different > protein fractions) altogether, isn't it? > > Would really appreciate if someone could enlighten on this, and > whether this can be gotten around by simply merging the some of the > smaller pepxml files in the first place. > > Thanks, > Bernt --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
