Mercurial > repos > bornea > nsaf_scoring

comparison nsaf_scoring.xml @ 7:71feabcbe3d2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bornea
date Tue, 17 May 2016 13:01:01 -0400
parents a2d0d346f07c
children f59b4984a974
comparison
equal deleted inserted replaced
6:5f09f5eeda75 7:71feabcbe3d2
34 </test> 34 </test>
35 </tests> 35 </tests>
36 <help> 36 <help>
37 NSAF Scoring Table 37 NSAF Scoring Table
38 ^^^^^^^^^^^^^^^^^^ 38 ^^^^^^^^^^^^^^^^^^
39 This tool is a static version of the APOSTL interactive affinity proteomics analysis software that calculates the NSAF, NSAF Score, and optionally the CRAPomePCT.
39 40
40 The NSAF score is the ratio of the NSAF for test preys versus control preys normalized by the number of controls. 41 The NSAF Score is the ratio of the NSAF for test preys versus control preys normalized by the number of controls.
41 The NSAF score performs similarly to the SaintScore in spectral counting data following a sigmoidal relationship 42 The NSAF Score performs similarly to the SaintScore in spectral counting data following a sigmoidal relationship
42 whereas with MS1 intensity data, NSAF scoring tracks sigmoidally to the log2 fold-change. The NSAF score is 43 whereas with MS1 intensity data, NSAF scoring tracks sigmoidally to the log2 fold-change. The NSAF score is
43 designed as a less stringent alternative to the SaintScore to complement the analysis, functioning as an empirical fold-change. 44 designed as a less stringent alternative to the SaintScore to complement the analysis, functioning as an empirical fold-change.
44 45
46 CRAPomePCT is the probability of a true interaction based on the abundance of a protein in the CRAPome database.
47
48 APOSTL was developed at H. Lee Moffitt Cancer Center and Research Institute and distributed under a GNU General Public License (GPL).
45 -------------- 49 --------------
46 50
47 **1) SAINT Output File** 51 **1) SAINT Output File**
48 52
49 SAINTexpress generated *list.txt* file. 53 SAINTexpress generated *list.txt* file.
57 should contain three columns: prey (protein) name, prey amino acid 61 should contain three columns: prey (protein) name, prey amino acid
58 length, and prey gene name. 62 length, and prey gene name.
59 63
60 **3) CRAPome File** 64 **3) CRAPome File**
61 65
62 Please specify an *CRAPome* file for Bubble Graph creation. An *Inter* 66 Please specify an *CRAPome* file for Bubble Graph creation. An *CRAPome*
63 file should contain five columns: IP name, Mapped Gene Symbol, Number of 67 file should contain five columns: IP name, Mapped Gene Symbol, Number of
64 Experiments (ratio), and Average spectral counts, and Max spectral counts. 68 Experiments (ratio), and Average spectral counts, and Max spectral counts.
65 69
66 **4) Interactions File** 70 **4) Interactions File**
67 71