Hi David, all my apologizes, the rar file got corrupted probably during the upload (the original on my HD was fine). I have uploaded again a zip file this time: lgillet_pepxml-again2.zip I hope that works this time (after download, I can decompress it back). Thanks for having a look at this issue. Best, Ludovic
On May 25, 7:24 pm, David Shteynberg <dshteynb...@systemsbiology.org> wrote: > Hi Ludovic, > > It seems the file you uploaded lgillet_pepxml_for_TPP4.3.rar is > corrupted. At least I am unable to open it. Please upload again. > > Thanks, > -David > > > > On Wed, May 19, 2010 at 2:54 AM, lgillet <gil...@imsb.biol.ethz.ch> wrote: > > Hi David, Hi Natalie, > > > I just posted the 4 pepxml files which give me the most striking > > differences in results between TPP-V4.0 and TPP-V4.3: > > lgillet_pepxml_for_TPP4.3.rar. I also posted the results > > (interact.pep.xml) which I obtain from running TPP-V4.0, TPP-V4.3 and > > TPP-V4.3 on scrambled file order (file #4>#3>#2>#1): lgillet_interact- > > results.rar. > > I really tried my best to figure out what the problem could be. > > Maybe you could re-run the same analyses (TPP-V4.0, TPP-V4.3, TPP-V4.3 > > with the scrambled file order) and let me know if you confirm my > > results or if there is something wrong maybe with the compiled version > > we have on our server (could still be a possibility). > > Finally, to answer Natalie's question, the differences are quite > > dramatic (to my opinion) between V4.0 and V4.3 (I would not have > > worried about 1-2% differences in IDs), but here, I am passing from 1% > > decoy (V4.0) to 23% decoy (V4.3) hits (at the same proba > 0.9). Also > > the number of unique peptides reported by V4.0 and V4.3 is quite > > different (2150 and 3161 resp.). Finally, many decoy hits pulled up in > > V4.3 with a prob>0.9 have actually a very bad MS/MS spectrum and a > > very low prob<0.01 (only reported if you use -p0 option) on V4.0. > > > Have a look at those MS/MS spectra for example: > > > 20100422_04_control_07.c.07700.07700.4 > > 20100422_04_control_07.c.02864.02864.3 > > > Let me know if you need any extra information. > > > Thanks a lot for your help on that. > > > Best, > > > Ludovic > > > On May 18, 11:21 pm, Natalie Tasman <natalie.tas...@insilicos.com> > > wrote: > >> Ludovic, > > >> Go ahead and post the files to the newsgroup's file area > >> (http://groups.google.com/group/spctools-discuss/files), and hopefully > >> one of the validation experts will take a look. > > >> I will point out that PeptideProphet uses random initialization for > >> it's curve fitting (EM algorithm). So it's not out of the question > >> that you'd see some small differences between runs on the same data > >> files, regardless of the order. Can you provide some measure of the > >> differences between runs for the reordered datasets? > > >> -Natalie > > >> On Tue, May 18, 2010 at 4:35 AM, lgillet <gil...@imsb.biol.ethz.ch> wrote: > >> > Hi everybody, > >> > I recently encountered a "bug" I think when people in my lab installed > >> > the newest TPP (v4.3 JETSTREAM rev 1, Build 201004201202 (linux)), > >> > especially when I try to confront the result to v4.0 which was our > >> > former "benchmark" version. > >> > When searching the same 4 pep.xml files with v4.0 and v4.3, I get an > >> > incredible difference in decoy hits number. For example, with v4.0, > >> > p>0.9, I would get my "regular" 1% decoy, while with v4.3, p>0.9, I > >> > get above 25% of decoys?!?? > >> > All the interact are run with the following options: xinteract -OApld - > >> > ddecoy *.pep.xml > >> > I could nail down the "problem" to the PeptideProphetParser which > >> > behaves very differently between v4.0 and v4.3, while InteractParser > >> > (which introduces the "is_rejected=1" tags) and RefreshParser do not > >> > influence the results. > >> > But at the moment, I do not know if it is an issue of the decoy > >> > statistical distribution of prophet or not... > > >> > One more thing that makes me even more suspicious is the fact that, > >> > only with TPP version 4.3, if you search those files in a difference > >> > order (let say: xinteract file1 file2 file3 Vs xinteract file3 file2 > >> > file1), you do get differences in the results as well?!? > > >> > I am willing to send the 4 pepxml where those observations are the > >> > most critical to David or Luis or anybody interested, but I truly > >> > believe that there might be something going wrong with the TPP v4.3. > > >> > Let me know to whom I should post the files. > > >> > Best regards, > > >> > Ludovic > > >> > -- > >> > You received this message because you are subscribed to the Google > >> > Groups "spctools-discuss" group. > >> > To post to this group, send email to spctools-disc...@googlegroups.com. > >> > To unsubscribe from this group, send email to > >> > spctools-discuss+unsubscr...@googlegroups.com. > >> > For more options, visit this group > >> > athttp://groups.google.com/group/spctools-discuss?hl=en. > > >> -- > >> You received this message because you are subscribed to the Google Groups > >> "spctools-discuss" group. > >> To post to this group, send email to spctools-disc...@googlegroups.com. > >> To unsubscribe from this group, send email to > >> spctools-discuss+unsubscr...@googlegroups.com. > >> For more options, visit this group > >> athttp://groups.google.com/group/spctools-discuss?hl=en. > > > -- > > You received this message because you are subscribed to the Google Groups > > "spctools-discuss" group. > > To post to this group, send email to spctools-disc...@googlegroups.com. > > To unsubscribe from this group, send email to > > spctools-discuss+unsubscr...@googlegroups.com. > > For more options, visit this group > > athttp://groups.google.com/group/spctools-discuss?hl=en. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > For more options, visit this group > athttp://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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