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Re: [Psidev-pi-dev] analysis tree
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From: Jones, A. <And...@li...> - 2008-05-28 11:33:36
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No I mean that there should be a generic DataFiltering protocol to define arbitrary data filtering operations. And yes, we need some examples of this for the CV and schema. But then this gets back to the problem that Martin highlighted of having multiple peptide and protein sets within one file... PeptideSet1 à DataFiltering à PeptideSet2 PeptideSet2 à ProteinDetection à ProteinSet1 ProteinSet1 à DataFiltering à ProteinSet2 Where ProteinSet2 is the “final” results... From: an...@it... [mailto:an...@it...] On Behalf Of Angel Pizarro Sent: 28 May 2008 12:30 To: Jones, Andy Cc: psi...@li... Subject: Re: [Psidev-pi-dev] analysis tree On Wed, May 28, 2008 at 7:25 AM, Jones, Andy <And...@li...> wrote: I do ;-) and am right there with you. Although to get at the question of user-defined thresholding, that in itself is an analysis, and should be communicated as such in the protocol + params. You mean peptide thresholding in the SpectrumIdentificationProtocol and protein thresholding in the ProteinDetectionProtocol? If so, we need examples of how this can be done using cvParams... No I mean that there should be a generic DataFiltering protocol to define arbitrary data filtering operations. And yes, we need some examples of this for the CV and schema. -angel From: an...@it... [mailto:an...@it...] On Behalf Of Angel Pizarro Sent: 28 May 2008 12:17 To: Jones, Andy Cc: psi...@li... Subject: Re: [Psidev-pi-dev] analysis tree On Wed, May 28, 2008 at 7:11 AM, Jones, Andy <And...@li...> wrote: Therefore, my vote is that we only support use case 1. This means that if someone wants to communicate a complete set of possible peptide / proteins (including decoys / likely false positives), it can be done, but this would be a separate file from their "final result set". Does everyone see what I'm getting at...? I do ;-) and am right there with you. Although to get at the question of user-defined thresholding, that in itself is an analysis, and should be communicated as such in the protocol + params. -angel Cheers Andy From: psi...@li... [mailto:psi...@li...] On Behalf Of Angel Pizarro Sent: 27 May 2008 16:53 To: Martin Eisenacher Cc: psi...@li... Subject: Re: [Psidev-pi-dev] analysis tree Still don't agree with this. In your last slide, both of the protein determinations are the result IMHO. If you want to highlight one or the other as "The Result" , create a file w/ just that analysis. -angel On Tue, May 27, 2008 at 11:42 AM, Martin Eisenacher <mar...@ru...> wrote: Dear colleagues! In the last Telecon I tried(!) to argument for an attribute marking the "actual" analysis of an AnalysisXML file. We agreed to let me assemble some descriptive slides (attached). I hope, with them my point gets more clear. I think it is not only a philosophical question, because it has consequences for programming, tools and databases... Bye Martin ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- Angel Pizarro Director, ITMAT Bioinformatics Facility 806 Biological Research Building 421 Curie Blvd. Philadelphia, PA 19104-6160 215-573-3736 ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- Angel Pizarro Director, ITMAT Bioinformatics Facility 806 Biological Research Building 421 Curie Blvd. Philadelphia, PA 19104-6160 215-573-3736 -- Angel Pizarro Director, ITMAT Bioinformatics Facility 806 Biological Research Building 421 Curie Blvd. Philadelphia, PA 19104-6160 215-573-3736 |
