I believe that my colleague, Luis Mendoza has implemented this on the models page in TPP 5.0.0 that is still pre-release.
-David On Thu, Jun 30, 2016 at 2:07 PM, Jesse <[email protected]> wrote: > David, > > Would it be too much to ask that those nice plots you replied with be > incorporated in the additional analysis info page where the FDR tables > are? I find that to be a very nice and quick way to assess my c-level > setting. > > Best, > Jesse > > On Monday, June 27, 2016 at 4:27:56 PM UTC-7, David Shteynberg wrote: >> >> Hello Jesse, >> >> As you noted, the CLEVEL used in your analysis is set to 5. This means >> that any PSM with an f-val not higher than 5 standard deviations from the >> estimated mean f-value of the false PSMs, will automatically be forced to a >> probability of 0 during modeling. This excludes all the high scoring >> DECOYS from further analysis since they are given a probability of 0. I >> would suggest you lower your CLEVEL value to achieve more PSMs with lower >> f-values but probabilities greater than 0 after PeptideProphet. It appears >> that the software is working as designed in this case. Normally you should >> set your CLEVEL as low as possible to give decent modeling without throwing >> away too many good PSMs. You should be able to get decent results with a >> much smaller CLEVEL on this dataset 0, 0.5 should all work well here, see >> attached. Also you can boost the correct peptide IDs if you enable the >> iProphet modeling and analysis on this data. >> >> Cheers, >> -David >> >> On Mon, Jun 27, 2016 at 3:52 PM, Jesse <[email protected]> wrote: >> >>> Also here are links to the pepxml files before and after peptide prophet: >>> >>> >>> https://drive.google.com/file/d/0B4N83JlasjgsemxITVZUNGpWdVk/view?usp=sharing >>> >>> >>> https://drive.google.com/file/d/0B4N83JlasjgsUE9iRmNEZU5zSEk/view?usp=sharing >>> >>> >>> On Monday, June 27, 2016 at 12:27:50 PM UTC-7, Jesse wrote: >>>> >>>> Hello TPP team, >>>> >>>> I've running some files through PeptideProphet using the xinteract >>>> interface, and I think I'm not getting enough decoy hits resulting in way >>>> too many correct IDs reported (evidenced by manual spectra review of >>>> hits). Please see the attached model results where no setting of min. >>>> Probability results in a 1% FDR and causes all results to be accepted. >>>> >>>> I think this is somehow related to the c-level parameter? I tried >>>> setting it even higher and that does decrease the IDs but there is always >>>> the same number of true hits (second attached screenshot). >>>> >>>> Otherwise, maybe I need to search my data with looser tolerances to get >>>> more decoy hits? >>>> >>>> Your help is appreciated. >>>> >>>> Best regards, >>>> Jesse >>>> >>> -- >>> 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 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 [email protected]. > To post to this group, send email to [email protected]. > 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
