Andreas,
Sorry, I forgot to mention you need to run ProphetModels.pl with the -k
option which will keep the intermediate data files (including the .tsv
files). These are used to plot the .png graphs, but deleted by defaulted
once done.
DT
andreas quandt wrote:
> hi dave,
>
> thanks for answering!
> i checked for ProphetModels.pl/ProtProphModels.pl but both do not create
> a .tsv file but rather .png files
> hence, i am a little bit confused...
>
>
> cheers,
> andreas
>
>
> Dave Trudgian wrote:
>
>> Andreas,
>>
>> We have a perl script which pulls out the relevant cut-offs from the
>> .tsv files created by ProphetModels.pl / ProtProphModels.pl using Linux
>> command line tools:
>>
>> # Peptide Prophet Calculated 1% FDR
>> $cmd = "gawk '\$4<=0.01 {print \$1}' interact.pep_FDR.tsv | sort | head
>> -n 1 ";
>> my $pep_pp_1pc_thresh = `$cmd` || "";
>>
>> #Peptide Decoy Estimated 1% FDR
>> $cmd = "gawk '\$5<=0.01 {print \$1}' interact.pep_FDR.tsv | sort | head
>> -n 1 ";
>> my $pep_decoy_1pc_thresh = `$cmd` || "";
>>
>> # Protein Prophet Calculated 1% FDR
>> $cmd = "gawk '\$4<=0.01 {print \$1}' interact.prot_FDR.tsv | sort | head
>> -n 1 ";
>> my $prot_pp_1pc_thresh = `$cmd` || "";
>>
>> # Protein Decoy Estimated 1% FDR
>> $cmd = "gawk '\$5<=0.01 {print \$1}' interact.prot_FDR.tsv | sort | head
>> -n 1 ";
>> my $prot_decoy_1pc_thresh = `$cmd` || "";
>>
>> Not elegant, but it works.
>>
>> DT
>>
>> andreas quandt wrote:
>>
>>
>>> dear list,
>>>
>>> i was wondering if there is a solution to calculate the probability
>>> cutoffs for s specific FDR such as 0.1%, 1%, 2.5%,...
>>>
>>> thanks for any answers!
>>>
>>> cheers,
>>> andreas
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>
>
> >
>
--
Dr. David Trudgian
Bioinformatician in Proteomics
University of Oxford
Tel: (+44) (01865 2)87807 (CCMP - Mon-Thu)
Tel: (+44) (01865 2)75557 (Dunn Sch - Fri)
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