I am facing problem in generating the ‘_psm_protFDR0.01_t_1.07.csv’ file,
although a file corresponding to FDR of 0.05 is generating. Is there any
way out to select the iProphet/PeptideProphet probability corresponding to
0.01 FDR.
I used following command line and got these results:
*C:/TPP/bin/Mayu.pl -verbose -PmFDR -A
c:/TPP/data/params/interact.ipro.pep.xml -C
c:/TPP/data/dbase/speclibs/Human_DECOY2.fasta -E rev_ -I 2 -M
c:/TPP/data/params/Mayu -P c: \TPP\data\params\mFDR=0.01:t*
C:\TPP\bin\Mayu.pl 1.07
initial DS cutoff: 0
status fdr: 0.01
INPUT:
using xml parser: 0
-A pepxml input: c:/TPP/data/params/interact.ipro.pep.xml
-B table input:
-C search database: c:/TPP/data/dbase/speclibs/Human_DECOY2.fasta
-D minimal peptide length: 0
TARGET-DECOY OPTIONS:
-E decoy id prefix: rev_
-F target to decoy ratio: 1
-G maximal PSM FDR for analysis: 0.01
-H PSM FDR steps: 11
PROTEIN FDR CALCULATION:
-I number of missed cleavages: 2
-J minimal peptide mass: 400
-K maximal peptide mass: 6000
-L number of protein size bins: 10
-N id set selection type: 0
all data and mFDR range (default)
don't correct identical sequences: 0
use equidist protein binning: 0
POST ANALYSIS:
run R analysis: 0
OUTPUT:
-P c:
file name base: c:/TPP/data/params/Mayu
print mFDR file: 1
print protein size bin file: 0
print protein feature file: 0
print input pepxml to csv: 0
print cumulative input to stdout: 0
print status: 0
------------------------------------
protein size
------------------------------------
parsing c:/TPP/data/dbase/speclibs/Human_DECOY2.fasta...
checking decoy ids for mirror target ids... some decoy entries do not have
corresponding target entries!
-> protein sizes have to be calculated for target and decoy sequences
236 total identical sequences, 132 sequences corrected to ''
42160 protein groups...
estimating protein sizes...
getting bins for the proteins...
------------------------------------
input PSM (mFDR)
------------------------------------
Found IprophetProbability. Using this instead of PeptideProphetProbability.
Caveat: Do not mix iprophet and peptideprophet files, there is no check!
interact.ipro.pep.xml parsed
0.00000% of PSM removed (length < 0 aa)
non FDR filtered target: 1213 PSM, 1061 peptides, 331 proteins
non FDR filtered decoy: 35 PSM, 34 peptides, 33 proteins
4.56731% of PSM removed (mFDR <= 0.01)
target: 1180 PSM, 1030 peptides, 301 proteins at 0.01 FDR
decoy: 11 PSM, 11 peptides, 11 proteins at 0.01 FDR
cumulative input data:
target: 1180 PSM, 1030 peptides, 301 proteins at 0.01 FDR
decoy: 11 PSM, 11 peptides, 11 proteins at 0.01 FDR
------------------------------------
protein identification FDR (protFDR)
------------------------------------
registered error models:
PSMFDR, PeptideIdFDR, ProteinIdFDR, LocalProteinIdFDR
DATA SELECTION SCHEME:
complete data set -> set of mFDR
1 total runs, looping through id sets...
------------------------------------
printing files
------------------------------------
main output files:
c:/TPP/data/params/Mayu_main_1.07.csv, c:/TPP/data/params/Mayu_main_1.07.txt
your desired mFDR 0.0144384754437265 for output (-P ...) is beyond the chosen
mFDR 0.01 used for calculations (-G ...) !
use a higher mFDR with -G for proper output (e.g. -G 0.0144384754437265)!
filtered data:
printing a set of filtered PSM to
c:/TPP/data/params/Mayu_psm_protFDR0.05_t_1.07.csv
filtering PSM with protFDR = 0.05, corresponding mFDR = 0.0144384754437265
keeping target PSM
1180 PSM printed out
91 seconds run time
Please help me out to resolve this problem.
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