Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide.
INFO: Calculating q values.
INFO: Final list yields 0 target peptides with q<0.1.
Does this mean that percolator did not find any significant target peptides ?
Also, I notice that Percolator by-default do not run target-decoy competition for separate target and decoy search. But in example on website, --post-processing-tdc is used.
I have a data output of crux which yields me no significant target peptides when target-decoy competition is used. However, if I use default mix-max method, I get significant target peptides. One more observation is that in target-decoy competition mode, even if I keep --testfdr 1.0, there are still no decoy in the decoy psms output file.
I notice that in the example of using tide and percolator for simple search on crux website, the percolator outputs:
Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide.
INFO: Calculating q values.
INFO: Final list yields 0 target peptides with q<0.1.
Does this mean that percolator did not find any significant target peptides ?
Also, I notice that Percolator by-default do not run target-decoy competition for separate target and decoy search. But in example on website, --post-processing-tdc is used.
I have a data output of crux which yields me no significant target peptides when target-decoy competition is used. However, if I use default mix-max method, I get significant target peptides.
One more observation is that in target-decoy competition mode, even if I keep --testfdr 1.0, there are still no decoy in the decoy psms output file.
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On Thu, Feb 20, 2020 at 1:36 AM Abhishek Dubey <abhishekdub...@gmail.com> wrote:I notice that in the example of using tide and percolator for simple search on crux website, the percolator outputs:
Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide.
INFO: Calculating q values.
INFO: Final list yields 0 target peptides with q<0.1.
Does this mean that percolator did not find any significant target peptides ?
Yes, I believe that is correct. I am cc'ing the Percolator team so they can comment on the precise semantics of this warning.
Also, I notice that Percolator by-default do not run target-decoy competition for separate target and decoy search. But in example on website, --post-processing-tdc is used.
I am not sure what example you are referring to. In general, if you want to use TDC you need to either run a concatenated target/decoy search or you need to enable post-processing-tdc. Otherwise, with a separate target/decoy search you can use the mix-max estimator.
I have a data output of crux which yields me no significant target peptides when target-decoy competition is used. However, if I use default mix-max method, I get significant target peptides.As long as you are using mix-max with separate targets and decoys, this should be fine. In general, mix-max offers slightly better statistical power than TDC.One more observation is that in target-decoy competition mode, even if I keep --testfdr 1.0, there are still no decoy in the decoy psms output file.I will let the Percolator folks comment on this one.
Bill
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On Monday, February 24, 2020 at 5:36:04 AM UTC+1, Bill Noble wrote:On Thu, Feb 20, 2020 at 1:36 AM Abhishek Dubey <abhishekdub...@gmail.com> wrote:I notice that in the example of using tide and percolator for simple search on crux website, the percolator outputs:
Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide.
INFO: Calculating q values.
INFO: Final list yields 0 target peptides with q<0.1.
Does this mean that percolator did not find any significant target peptides ?
Yes, I believe that is correct. I am cc'ing the Percolator team so they can comment on the precise semantics of this warning.Yes, that is correct.Also, I notice that Percolator by-default do not run target-decoy competition for separate target and decoy search. But in example on website, --post-processing-tdc is used.
I am not sure what example you are referring to. In general, if you want to use TDC you need to either run a concatenated target/decoy search or you need to enable post-processing-tdc. Otherwise, with a separate target/decoy search you can use the mix-max estimator.
I have uploaded the stderr, target psms and decoy psms for both mixmax and tdc :