Hi David, Thanks for your kind help. Actually I am estimating the FDR by using the Mayu tool, after combining the iprophet results of all the three datasets which I have, as this gives me single Posterior probability (PPs/IPs) that I am using in the SpectraST command line so as to generate the spectral library. Yes, I got the point which you have highlighted, but can I use Mayu for estimating the FDR at final stage and then filter the results below the threshold PP of FDR less than 1%, instead of filtering the results at each iProphet analyses?
Thanks Ankit On Fri, 5 Apr 2019 at 20:03, David Shteynberg < [email protected]> wrote: > Hello Ankit, > > If you computer has the resources to handle all files then running one > iProphet job to combine the results will give you one analysis result with > FDR rates that apply to all the data. If you do multiple iProphet runs > then you have to be more careful about how you combine the results because > your runs will overlap more in the correct result than the incorrect > results so simply taking all results together above an FDR threshold will > inflate your final FDR. One easy way to do this is to divide the FDR by > the number of iProphet runs being combined. For example if you split the > results into two iProphet analyses and you want the combined FDR to be less > than 1% you would filter each iProphet analyses at 0.5% FDR and then take > the total set. Does that make sense? > > Cheers, > -David > > On Thu, Apr 4, 2019 at 8:57 AM Ankit Balhara <[email protected]> > wrote: > >> Thanks Felipe. >> >> I have posted this issue in the issues section of DIA-Umpire issue >> tracker. >> >> Ankit >> >> >> >> On Thu, 4 Apr 2019 at 19:21, Felipe da Veiga Leprevost < >> [email protected]> wrote: >> >>> Hi Ankit; >>> >>> Please feel free to submit your DIA-Umpire questions and issues to our >>> DIA-Umpire issue tracker: https://github.com/Nesvilab/DIA-Umpire >>> >>> Regards >>> >>> On Wednesday, April 3, 2019 at 7:05:59 AM UTC-4, Ankit Balhara wrote: >>>> >>>> Hi All, >>>> >>>> I am analyzing the SWATH-MS data using the DIA-Umpire. And I have 3 >>>> data files of same sample which lead to generation of 9 .mgf output files >>>> from DIA-Umpire, which were converted into 9 mzXML and then subjected to >>>> Comet and X! Tandem search, and subsequently to peptide prophet and hence >>>> total files generated during this process are 18 pep.xml files. >>>> My ultimate aim to build the assay library. So, I am confused how to >>>> combine the results of these 18 peptideprophet files. >>>> >>>> Should I combine the Comet search results of each data file separately >>>> and X! Tandem results separately and then combine these outputs again using >>>> iProphet? This should result in generation of 3 iprophet result files >>>> corresponding to each data file, which can again combined into one file by >>>> iProphet in final step? >>>> >>>> Or there is another way out of this problem? >>>> >>>> Thanks >>>> >>>> Ankit >>>> >>> -- >>> 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. > -- 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.
