Hi Jimmy, I was following Elias & Gygi's formula for concatenated searches. I was unaware that the same formula is to be used for both searches. Please provide me with the reference.
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 Fri, Nov 26, 2010 at 12:03 AM, Jimmy Eng <[email protected]> wrote: > It should be number(decoys)/number(targets) irrespective of > concatenated or separate searches. > > On Wed, Nov 24, 2010 at 5:20 AM, Amit Yadav <[email protected]> > wrote: > > Hi, > > > > From what I understand, the simplest ways to calculate FDR using a > > Target-Decoy search are:- > > > > 1. Run a Concatenate target and decoy database search. The formula > > would be : 2 *number(decoys)/ number(target+decoys) - See Elias > > and Gygi , Nat Methods. 2007 Mar;4(3):207-14. > > > > 2. Run Separate target and decoy searches. The formula would be: > > number(decoys)/number(targets). See Kall et al J Proteome Res. 2008 > > Jan;7(1):29-34 > > > > I think your formula should be the first one. Members, please correct > > me if I am wrong. > > > > Regards, > > > > Amit Kumar Yadav > > Senior Research Fellow (SRF-CSIR) > > IGIB, New Delhi (India) > > > > MassWiz Web server > > MassWiz sourceforge project > > MassWiki > > > > > > > > On Wed, Nov 24, 2010 at 6:39 PM, Bjorn <[email protected]> wrote: > >> > >> Hello all, > >> > >> I am trying to find my way through the different interpretations and > >> calculations of the FDR, but I'm a bit lost where it comes to the > >> PeptideProphet. > >> > >> So far, I know that the simplest calculation is (decoy_hits/ > >> target_hits). So, I ran X!tandem on my dataset (target DB + > >> concatenated decoy DB) and then ran PeptideProphet on the resulting > >> pep.xml file (not setting the decoy option!). > >> I then set a certain probability threshold (say 0.85) and looked at > >> the number of spectra (e.g. 1200 of 1500). Setting the protein text to > >> decoy gives me, e.g. 50 hits. The FDR for a prob. of 0.85 would then > >> be 50/1150. If I look at the table displayed in the PeptideProphet, > >> the FDR I found is almost spot-on with the number in the table. The > >> thing is that if I lower my probabilty threshold, the FDRs in the > >> table stay relatively low, while the FDRs I calculate with the above > >> formula go up. Is there any extra correction being done in the > >> PeptideProphet (like correct for the percentage of incorrect target > >> hits (PIT) as described by Kall et al in 2008)? > >> Or am I missing something vital here? > >> > >> Furthermore, how is the estimated number of correct assignments > >> calculated? I can't seem to find the correct formula to come to that > >> number? I assume it is related to the surface under the curve plotted > >> with the correct identifications? > >> > >> Many questions, but I hope someone can help me with this. > >> > >> Best regards, > >> > >> bjorn > >> > >> -- > >> 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]<spctools-discuss%[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. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to > [email protected]<spctools-discuss%[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. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]<spctools-discuss%[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. 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.
