changeset 5:a2d0d346f07c draft

Uploaded

--- a/nsaf_scoring.xml	Wed May 11 10:53:40 2016 -0400
+++ b/nsaf_scoring.xml	Wed May 11 12:51:46 2016 -0400
@@ -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>
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