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 <[email protected]<javascript:> > > 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). >> >> 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 [email protected] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
