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.
