Yes, provided u are using Elias and Gygi method (concatenated search). Regards,
*Amit Kumar Yadav * Senior Research Fellow (SRF-CSIR) IGIB, New Delhi (India) *MassWiz Web server* <http://masswiz.igib.res.in> * <http://masswiz.igib.res.in>**MassWiz sourceforge project*<https://sourceforge.net/projects/masswiz> * <https://sourceforge.net/projects/masswiz>**MassWiki*<https://sourceforge.net/apps/mediawiki/masswiz/index.php?title=MassWiki> On Thu, Mar 28, 2013 at 10:16 PM, Hanice Sun <sunhan...@gmail.com> wrote: > Dear Amit, > > I should sort all the spectrum-peptide matching in one raw file by e-value > from low to high, than cut the FDR? > Am I right? > Thank you very much. > > > On Friday, March 29, 2013 12:26:06 PM UTC+8, Amit Kumar Yadav wrote: > >> Hi, >> >> Interpretation of e-values will always be coupled to the database size >> (more appropriately, the size of candidates for a particular spectrum). So, >> I do not think it is the correct metric for controlling false positives. >> >> When the authors had suggested using e-values, I believe FDR was not in >> use (much). But after it was necessary to control for global error rates, >> Target-Decoy may be your best option. In my experience, e-values are better >> normalized/calibrated ( i don't know what is the right term for this) to >> spectrum to spectrum variations than hyperscore, it is better to use >> e-values than hyperscore for FDR calculation. Hyperscore have more >> variations and suffer from peptide length bias. >> >> >> Regards, >> >> *Amit Kumar Yadav * >> Senior Research Fellow (SRF-CSIR) >> IGIB, New Delhi (India) >> >> *MassWiz Web server* <http://masswiz.igib.res.in> >> * <http://masswiz.igib.res.in>**MassWiz sourceforge >> project*<https://sourceforge.net/projects/masswiz> >> * >> <https://sourceforge.net/projects/masswiz>**MassWiki*<https://sourceforge.net/apps/mediawiki/masswiz/index.php?title=MassWiki> >> >> >> On Thu, Mar 28, 2013 at 1:30 AM, Hanice Sun <sunh...@gmail.com> wrote: >> >>> I am considering using target-decoy FDR or directly using E-value of >>> x!tandem? >>> >>> It seems that xtandem author recommend the latter. >>> >>> *(* >>> *This reference describes the idea of using reversed sequences to >>> validated large collections of protein identifications. The GPM has this >>> method built-in as a possible method for validation.* >>> *N.B.: We strongly recommend that you do not use this type of method >>> for any purpose other than comparison with other search engines. The >>> "decoy" search methods that have been developed from this manuscript are >>> deeply flawed algorithms for determining the confidence of peptide >>> identification assignments.* >>> *)* >>> >>> >>> However, >>> >>> 1. If I use E-value, I don't know which threshold should I set. >>> Although I tried to understand E-value, I still cant know which value is >>> suitable. >>> >>> At the beginning , I thought maybe I could set it as 1e-3, but I found >>> the default E-value of blast is 10, and this paper uses 100 ( >>> http://www.ncbi.nlm.nih.gov/**pubmed/18216375<http://www.ncbi.nlm.nih.gov/pubmed/18216375> >>> ). >>> >>> So I dare not set this threshold. >>> >>> 2. If I choose the target-decoy strategy, I don't know which value >>> should I use to sort the matching, could I use hyper-score? >>> >>> Could anyone help me? thank you very much. >>> >>> ps. My database is relatively large , It may affect the choice. >>> >>> -- >>> 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-discu...@**googlegroups.com. >>> To post to this group, send email to spctools...@googlegroups.**com. >>> >>> Visit this group at http://groups.google.com/** >>> group/spctools-discuss?hl=en<http://groups.google.com/group/spctools-discuss?hl=en> >>> . >>> For more options, visit >>> https://groups.google.com/**groups/opt_out<https://groups.google.com/groups/opt_out> >>> . >>> >>> >>> >> >> -- > 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 http://groups.google.com/group/spctools-discuss?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- 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 http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
