Opened 9 years ago

Closed 8 years ago

Last modified 2 years ago

#773 closed (fixed)

Optimisation of hits combination

Reported by: Fredrik Levander Owned by: Fredrik Levander
Milestone: Proteios SE 2.17.0 Keywords:
Cc:

Description (last modified by Fredrik Levander)

The combined hits report (#163) needs to be optimised to accomodate batches of large search results (#755).

Change History (23)

comment:1 Changed 9 years ago by Fredrik Levander

(In [4270]) Refs #773. Updated querying for peptide-based non-gel reports.

comment:2 Changed 9 years ago by Fredrik Levander

(In [4271]) Refs #773. Updated sorting and some loops for better performance.

comment:3 Changed 9 years ago by Fredrik Levander

(In [4272]) Refs #773. Updated FDR calculation for performance.

comment:4 Changed 9 years ago by Fredrik Levander

(In [4273]) Refs #773. Corrected minor bug.

comment:5 Changed 8 years ago by Fredrik Levander

Resolution: fixed
Status: newclosed

comment:6 Changed 8 years ago by Fredrik Levander

(In [4350]) Refs #773. Refined q-value calculation.

comment:7 Changed 8 years ago by Fredrik Levander

Resolution: fixed
Status: closedreopened

Run into memory problems with a table of more than 1000000 identified peptides

comment:8 Changed 8 years ago by Fredrik Levander

Description: modified (diff)

comment:9 Changed 8 years ago by Fredrik Levander

(In [4360]) Refs #773. Added logging.

comment:10 Changed 8 years ago by Fredrik Levander

(In [4361]) Refs #773. Small optimisation of score counting. And more logging.

comment:11 Changed 8 years ago by Fredrik Levander

(In [4362]) Refs #773. Further optimisation of counting.

comment:12 Changed 8 years ago by Fredrik Levander

Resolution: fixed
Status: reopenedclosed

(In [4363]) Fixes #773. Optimisation of iteration when combining.

comment:13 Changed 5 years ago by Fredrik Levander

(In [4591]) Refs#773. Added some DB queries to keep connection open for large datasets.

comment:14 Changed 5 years ago by Fredrik Levander

(In [4592]) Refs #773. Added further DB queries to keep connection open for large datasets.

comment:15 Changed 5 years ago by Fredrik Levander

(In [4594]) Refs #773. Bug fix for optimisation

comment:16 Changed 5 years ago by Fredrik Levander

(In [4595]) Refs #773. Further optimisation

comment:17 Changed 5 years ago by Fredrik Levander

(In [4604]) Refs #773. Some further optimisation and refactoring

comment:18 Changed 5 years ago by Fredrik Levander

(In [4606]) Refs #773. More status updates for long jobs.

comment:19 Changed 5 years ago by Fredrik Levander

(In [4607]) Refs #773. Update to speed up FDR approximation when many decoys have been matched.

comment:20 Changed 4 years ago by Fredrik Levander

(In [4619]) Refs #773. Removed No score option and, and changed default to peptide level report and keeping decoys,.

comment:21 Changed 4 years ago by Fredrik Levander

(In [4625]) Refs #773. Updated report to display also peptide FDR and not only PSM FDR for combined hits.

comment:22 Changed 4 years ago by Fredrik Levander

(In [4626]) Refs #773. Updated phrasing in report to use target and decoy database instead of standard and random database.

comment:23 Changed 2 years ago by Fredrik Levander

(In [4643]) Refs #773. Adding possibility to process all samples separately when calculating FDRs to increase performance.

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