Hi David, Thanks a lot, then it should be the issue of repeating spectrum name. In this case, each spectrum has two rank one hits, one from decoy sequences and the other one is from Target sequences.
Thanks, Chih-Chiang On Apr 4, 2017 4:53 PM, "David Shteynberg" < [email protected]> wrote: > The message: > > "Found 4823 Decoys, and 4820 Non-Decoys" suggests there a no correct > result in this dataset if the decoy database contains 50% decoy sequences. > Does this suggest your Decoy Search contains only Decoys? If you have no > correct results in the search you would still expect half of your random > (incorrect) hits to be to the Target proteins. Can you double check you > Decoy/Target concatenated database to make sure both Decoys and Targets are > present. > > The ERROR is possible due to several possibilities. First of all, which > version of the TPP are you on and what options are you using for > xinteract? It is possible that the repeating spectrum names are confusing > PeptideProphet. > > Thanks, > -David > > On Tue, Apr 4, 2017 at 11:39 AM, Chih-Chiang Tsou < > [email protected]> wrote: > >> The decoys are just reversed sequences. I am performing non-specific >> digestion search, so the chance that spectrum get high-scoring decoy hit is >> much higher than tryptic peptide search. >> >> I tried the approach I mentioned by doing two searches, one was searching >> against only foward-sequence, and then other searching against >> reversed-sequences (Comet search engine). Then in xinteract I specified two >> input pep.xml files and use -D option to link to the combined FASTA file. >> But the program stopped and gave error message "NAN probability density >> detected". Any suggestions? >> >> xinteract output: >> Found 4823 Decoys, and 4820 Non-Decoys >> Initialising statistical models ... >> Iterations: ...ERROR: NAN probability density detected. >> >> Thanks, >> Chih-Chiang >> >> On Tuesday, April 4, 2017 at 11:20:40 AM UTC-5, David Shteynberg wrote: >>> >>> It sounds like a problem with the way your decoys might be getting >>> generated. How do you generate the decoy? >>> >>> On Tue, Apr 4, 2017 at 8:59 AM, Chih-Chiang Tsou <[email protected]> >>> wrote: >>> >>>> Hi David, >>>> >>>> Thanks for the prompt response. >>>> So what I am trying to do is to avoid decoy hit Blocking the possible >>>> true hit. >>>> >>>> The way I perform the analysis is to search data against a FASTA file >>>> which has reversed sequences appended. Then during PeptideProphet analysis >>>> I specify the decoy prefix and in the end use the probabilities for >>>> target/decoy hits to estimate FDR. One potential problem for me is that if >>>> a spectrum happens to match a decoy as best hit, with a very high score >>>> let's say XCorr 2.0, and the second hit with Xcorr 1.9, which si actually >>>> the true hit, would be discarded after PeptideProphet analysis. >>>> >>>> If PeptideProphet takes only top hit, could I do two separate searches >>>> using target-FASTA and Decoy-FASTA and specify two input files in >>>> PeptideProphet? Any suggestions? >>>> >>>> >>>> Thanks, >>>> Chih-Chiang >>>> >>>> On Tuesday, April 4, 2017 at 9:45:11 AM UTC-5, David Shteynberg wrote: >>>>> >>>>> No. It uses the top hit only. >>>>> >>>>> On Tue, Apr 4, 2017 at 7:34 AM, Chih-Chiang Tsou <[email protected] >>>>> > wrote: >>>>> >>>>>> Hi >>>>>> >>>>>> Is there any option in xinteract to tell PeptideProphet take topN >>>>>> hits for each spectrum for probability calculation? >>>>>> >>>>>> Thanks, >>>>>> Chih-Chiang >>>>>> >>>>>> -- >>>>>> 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 [email protected]. >>>>>> To post to this group, send email to [email protected]. >>>>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>> >>>>> >>>>> -- >>>> 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 [email protected]. >>>> To post to this group, send email to [email protected]. >>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >> 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 [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- > You received this message because you are subscribed to a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit https://groups.google.com/d/ > topic/spctools-discuss/uCFD9-d1c0c/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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