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nsaf_scoring.xml |
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| diff -r 9ff511e32040 -r a2d0d346f07c nsaf_scoring.xml --- a/nsaf_scoring.xml Wed May 11 10:53:40 2016 -0400 +++ b/nsaf_scoring.xml Wed May 11 12:51:46 2016 -0400 |
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| @@ -34,5 +34,41 @@ </test> </tests> <help> +NSAF Scoring Table +^^^^^^^^^^^^^^^^^^ + +The NSAF score is the ratio of the NSAF for test preys versus control preys normalized by the number of controls. +The NSAF score performs similarly to the SaintScore in spectral counting data following a sigmoidal relationship +whereas with MS1 intensity data, NSAF scoring tracks sigmoidally to the log2 fold-change. The NSAF score is +designed as a less stringent alternative to the SaintScore to complement the analysis, functioning as an empirical fold-change. + +-------------- + +**1) SAINT Output File** + +SAINTexpress generated *list.txt* file. + + **Note:** Prey IDs must be in Uniprot/Swissprot format (e.g. + "EGFR\_HUMAN" or "P00533"). + +**2) Prey File** + +Please specify a *Prey* file for Bubble Graph creation. A *Prey* file +should contain three columns: prey (protein) name, prey amino acid +length, and prey gene name. + +**3) CRAPome File** + +Please specify an *CRAPome* file for Bubble Graph creation. An *Inter* +file should contain five columns: IP name, Mapped Gene Symbol, Number of +Experiments (ratio), and Average spectral counts, and Max spectral counts. + +**4) Interactions File** + +Please specify an *Inter* file for Bubble Graph creation. An *Inter* +file should contain four columns: IP name, bait name, prey name, and +spectral counts or intensity values, depending on the mode of +quantification. + </help> </tool> \ No newline at end of file |