I am not convinced that turning this model off creates a huge difference. You can run the analysis both ways and consider the best results.
On Tue, Mar 1, 2016 at 1:38 PM, John Damask <jbdam...@gmail.com> wrote: > Hello David, > Thanks very much for your response. > > Your slides from a TPP course (a couple of years old, now) state that > iProphet's NSP model "Should be turned off when ProteinProphet NSP model > is used". Is this still the recommendation? In the post I originally > linked to, wrt NSP in iProphet and ProteinProphet, you state that you "have > not found the two to interfere" which reads to me like it can be used in > both. > > John > > > On Friday, February 19, 2016 at 2:24:06 PM UTC-5, David Shteynberg wrote: >> >> Hello John, >> >> Thank you for your question. >> >> NSP in iProphet looks at all proteins that a given peptide matches, it >> then sums the probabilities of all the other peptides that match the same >> protein. For a given peptide it then takes as the NSP the maximum such sum >> over all the proteins matched. It is a bit different from NSP in >> ProteinProphet since in ProteinProphet a given peptide has a different NSP >> in each protein it appears. >> >> -David >> >> On Fri, Feb 19, 2016 at 11:04 AM, John Damask <jbda...@gmail.com> wrote: >> >>> Hi, >>> >>> I'm interested in learning more about how iProphet's NSP model works. >>> The original paper doesn't discuss it as a first class iProphet model and >>> Fig1 only shows it in ProteinProphet. >>> >>> In this post >>> <https://groups.google.com/forum/#!searchin/spctools-discuss/iprophet$20nsp/spctools-discuss/mLAMdJUP8AQ/wGQfI0061scJ> >>> David states "I have found that applying the NSP model at the iProphet step >>> greatly improves performance on peptide level". But what is it doing, >>> exactly? >>> >>> Thanks for providing such great software to the community! >>> John >>> >>> -- >>> 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 spctools-discu...@googlegroups.com. >>> To post to this group, send email to spctools...@googlegroups.com. >>> Visit this group at https://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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
