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Enhancement - iTRAQ - Search score #6

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
The search score parameter is very dependent on these being files from mascot 
where you can recognize the Mascot score. If we support other search engines, 
we would like to support thresholding by another score - say "FDRScore < 0.01", 
p-value < 0.05, e-value < 0.01. 

However, there is quite a long list of possible scores that could be found in 
an mzid file - all sourced from here (PSI-MS CV):

http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabu
lary/psi-ms.obo

Any CV term flagged as follows:

is_a: MS:1001143 ! search engine specific score for peptides

Would be valid for use in applying a threshold. We could cache a local version 
of the PSI-MS (or download from the website at intervals) and parse out all 
these terms, using them to populate a drop down? Fawaz coded something like 
this for the ProteoIDViewer.

Original issue reported on code.google.com by andrewro...@googlemail.com on 17 Oct 2012 at 9:23

GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
This still needs to be implemented. Xtracker relies upon passThreshold="true" 
and rank=1 for quantification purposes. 

We need to (offer to) run mzidLib:Threshold as pre-processing, which accepts a 
CV parameter, lowToHigh true|false, and the score threshold to use as 
parameters.

We might also offer to run mzidfLib:FalseDiscovery pre-processing as well, so 
that we can set FDR at 1% for example.

Original comment by andrewro...@googlemail.com on 21 Nov 2013 at 12:49