Thanks so much David for your response. It makes sense. All the best, Soroush
On Wednesday, January 20, 2021 at 11:54:12 PM UTC-5 David Shteynberg wrote: > This option changes the way mixture models in the TPP (PeptideProphet) are > generated. The probabilities are estimated based on the mixture models > learned by PeptideProphet. When the mixture models change so will the > probabilities. > > On Wed, Jan 20, 2021 at 8:44 PM Soroush F <[email protected]> wrote: > >> Dear David, >> >> Thanks so much for your time answering my questions. >> >> I gather from your answer that this option is for TPP. If that is the >> case, why does the PeptideProphet probabilities changes when selecting the >> option? Am I missing something? >> >> Many thanks. >> Soroush >> >> On Tuesday, January 19, 2021 at 2:59:56 PM UTC-5 David Shteynberg wrote: >> >>> Dear Soroush, >>> >>> This option makes use of the TPP's semi-supervised learning mode, which >>> can be used in conjunction with semi-parametric mode, at the user's >>> discretion. Until now, some search engines supported by TPP analysis could >>> only be modeled by PeptideProphet using semi-parametric and semi-supervised >>> that required decoys to be used in the search. Going forward with the new >>> version of the TPP (pre-release version 6.0.0) this is not going to be >>> the case as we will be providing both types of models for more search >>> engine results. I hope this answers your question. >>> >>> Cheers, >>> -David >>> >>> On Mon, Jan 18, 2021 at 4:02 PM Soroush F <[email protected]> wrote: >>> >>>> Dear all, >>>> >>>> I was wondering when one should use "Use decoy hits to pin down the >>>> negative distribution" in the Peptide Prophet (run through Petunia)? >>>> >>>> If I want to use Target-Decoy approach to estimate FDR in my analysis, >>>> should I use this box, or it has nothing to do with it? >>>> >>>> Thanks, >>>> Soroush >>>> >>>> -- >>>> 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 view this discussion on the web visit >>>> https://groups.google.com/d/msgid/spctools-discuss/4592e133-201d-4893-9573-ddee56f1071dn%40googlegroups.com >>>> >>>> <https://groups.google.com/d/msgid/spctools-discuss/4592e133-201d-4893-9573-ddee56f1071dn%40googlegroups.com?utm_medium=email&utm_source=footer> >>>> . >>>> >>> -- >> 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 view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/a33abb3e-ee23-43f8-aab0-af0c7717b676n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/a33abb3e-ee23-43f8-aab0-af0c7717b676n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/f59fdce7-4bed-4d98-8259-18f28e9bb815n%40googlegroups.com.
