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 <[email protected]> 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 <[email protected]> > 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 <[email protected]> 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 [email protected]. >> > To unsubscribe from this group, send email to >> > [email protected]. >> > 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 [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> 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 [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. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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