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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