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.
