Hi David, Thanks for your response, I realised the xinteract has to be used with *.pep.xml behind the options. Previously I used it before the options. It manages to generate a working interact.pep.xml with all the PeptideProphet probabilities. But the .shtml file showed an error:
http://localhost/ISB/data/OC/OGEmRPTD10/OGEmRPTD10_Tandem_interact.pep.shtml [an error occurred while processing this directive] This is not a big problem for me. I can live with it. The problem that remains is the ion spectra could not be viewed in the PepXML browser. I have put it in a separate post, since it should not be due to the reason of combining >100 pep.xml files on the command line. Thanks for your help too, Brian. Bernard On Jul 3, 2:24 am, David Shteynberg <[email protected]> wrote: > 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 -~----------~----~----~----~------~----~------~--~---
