Hi David, Thanks so much for your reply. Below is my PeptideProphet parameters. Could you please tell me how to set the parameters to let PeptideProphet to use the decoy PSMs to model the negative distribution?
<https://lh5.googleusercontent.com/-DH7DhSNAtrw/U1n3Qf_m37I/AAAAAAAADMM/GNj3RCPHDpE/s1600/QQ%E6%88%AA%E5%9B%BE20140425134944.png> Many thanks and best regards! Bo 在 2014年4月25日星期五UTC+8上午12时16分59秒，David Shteynberg写道： > > This indicates that Decoy estimated Error Rate is 0, at all PeptideProphet > probabilities greater than 0, given the Decoys you are using. Are you > giving Decoy tags to PeptideProphet when you run it? If PeptideProphet > knows an ID is a Decoy it will give it a probability of 0 (unless you > specify the advanced -Od flag which allows reporting of known Decoy > probabilities) and you will not be able to use the Decoys a second time > like you are trying here. Either try the -Od flag or separate your Decoys > in to two independent sets of which only one will be known Decoys. The > Decoy Database tool in the TPP will do this for you. > > Cheers, > -David > > > On Thu, Apr 24, 2014 at 7:51 AM, Bo <[email protected] <javascript:>>wrote: > >> >> Hi, >> >> I have run the following command line: >> >> >> <https://lh6.googleusercontent.com/-O1uMOERRjgs/U1kkKGEEPiI/AAAAAAAADL0/JtFvafGYfRA/s1600/QQ%E6%88%AA%E5%9B%BE20140424225037.png> >> >> But I got a figure like below. The result is very odd. Does any one know >> what's problem? >> >> >> >> <https://lh4.googleusercontent.com/-eMjzhGHyQ58/U1kju28jqSI/AAAAAAAADLs/COYbaVa7bA0/s1600/msgf_interact.pep_ROC.png> >> >> Many thanks and best regards! >> >> Bo >> >> -- >> 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. >> 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.
