What was the problem with the final generated interact.pep.xml file? Can you verify that all of your pep.xml files are complete? Check their size and starting and ending tags for completeness. If there are any error message please post them here.
-David On Thu, Jul 2, 2009 at 10:40 AM, Brian Pratt<[email protected]> wrote: > > 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 -~----------~----~----~----~------~----~------~--~---
