In order to see the Decoys in your results with non zero problem you either need two Decoy sets with different prefix or to use option -Od in xinteract. On Mar 6, 2015 7:49 AM, "David Shteynberg" < [email protected]> wrote:
> This seems like a strange problem. Are you describing model estimates or > Decoy counts here? I would recommend carefully looking at the model to > decoys FDR plots and the individual models both from PeptideProphet for > each of the searches and iProphet. It could be a misbehaving search engine > or incorrect assumption in the iProphet modeling that would require turning > off. I am not sure. If you can share the data I could explore further. > > -David > On Mar 6, 2015 5:17 AM, "Florian" <[email protected]> wrote: > >> Dear list, >> >> I am trying to incorporate multiple database search engines and iProphet >> into my data analysis. I run the TPP from commandline with following >> commands: >> >> 1) For single search engines (here: X!Tandem): >> xinteract -Ninteract_xtandem.pep.xml -p0.05 -l7 -OARP -dSHUFFLED >> -X-m0.02-nK,6.031817-nn,6.031817-H *.pep.xml >> ProteinProphet interact_xtandem.pep.xml interact_xtandem.prot.xml XPRESS >> EXCLUDE_ZEROS >> >> 2) To use iProphet on this single database search engines: >> xinteract -Ninteract_xtandem.pep.xml -p0.05 -l7 -OARP -dSHUFFLED >> -X-m0.02-nK,6.031817-nn,6.031817-H *.pep.xml >> c:\Inetpub\tpp-bin\InterProphetParser \Xtandem\interact_xtandem.pep.xml >> interact.ipro.pep.xml >> ProteinProphet interact.ipro.pep.xml interact_xtandem.ipro.prot.xml >> XPRESS EXCLUDE_ZEROS IPROPHET >> >> 3) For multiple search engines (here: X!Tandem and MSGF+): >> c:\Inetpub\tpp-bin\InterProphetParser \Xtandem\interact_xtandem.pep.xml >> \MSGF\interact_msgf.pep.xml interact.ipro.pep.xml >> RefreshParser interact.ipro.pep.xml %dbase% >> ProteinProphet interact.ipro.pep.xml interact_ipro.prot.xml XPRESS >> EXCLUDE_ZEROS IPROPHET >> >> 4) For testing, I also ran ProteinProphet on the combined iProphet output >> without using the IPROPHET option: >> c:\Inetpub\tpp-bin\InterProphetParser \Xtandem\interact_xtandem.pep.xml >> \MSGF\interact_msgf.pep.xml interact.ipro.pep.xml >> RefreshParser interact.ipro.pep.xml %dbase% >> ProteinProphet interact.ipro.pep.xml interact_ipro.prot.xml XPRESS >> EXCLUDE_ZEROS >> >> In an example analysis, I identified the following number of Proteins >> after using <1% FDR based on the ProteinProphet estimation: >> 1a) X!Tandem only: 3,657 Proteins (589 single hits) >> 1b) MSGF+ only: 3,791 Proteins (614 single hits) >> 2a) X!Tandem with iProphet: 3,325 (735 single hits) >> 2b) MSGF+ with iProphet: 3,473 Proteins (773 single hits) >> 3) X!Tandem, MSGF+ and iProphet: 3,803 Proteins (964 single hits) >> 4) X!Tandem, MSGF+ without IPROPHET option: 4,220 proteins (732 single >> hits) >> >> It seems like iProphet reduces the number of protein IDs, while >> increasing the single hits. So, if I substract the single hits, I even get >> less protein IDs when using two database search engines instead of one. It >> even gets worse when I use Myrimatch together with X!Tandem and MSGF+. How >> can that be? Did I do some obvious mistake here? Or do I have to switch off >> single models of the iProphet? >> >> If not, is it acceptable to use iProphet output without the IPROPHET >> option in ProteinProphet? This way, I can use multiple search engines and >> INCREASE my IDs, instead of loosing some. >> >> Many thanks! >> >> >> >> >> -- >> 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. >> 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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
