Hi All, I have 2 questions I'd be grateful if people could help answer:
1) Is it valid to combine multiple iprophet.pep.xml files by passing through iprophet for a second time? - alternatively, is it valid to combine a single iprophet.pep.xml file with interact.pep.xml files in iprophet? I am trying to combine a lot of different experiments / search engines results etc, and have been combining in iprophet - but I appear to have maxed out the number interact.pep.xml files to pass into iprophet. Beyond a certain number of files (doesn't appear to be file-specific), iProphet fails. As a workaround, I wondered if I could simply run half of the files through iProphet, then combine the resulting file with the remaining files to be run, by running iprophet again prior to running protein prophet. - Would this be valid? 2) I attended a TPP course last year in which the course notes stated that NSP should be switched off in iProphet, if NSP model is to be used in protein prophet. I am using petunia (running protein prophet on the iprophet results), and I cannot see a NSP option in the protein prophet parameters. Does this mean that NSP is not being used when I run protein prophet? ... (i.e. am I ok to leave NSP on in iProphet?) Thanks Pete -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
