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
>>
>>
>>
>>
>>
>
>
>
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