Mercurial > repos > bornea > nsaf_scoring
comparison nsaf_scoring.xml @ 5:a2d0d346f07c draft
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author | bornea |
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date | Wed, 11 May 2016 12:51:46 -0400 |
parents | e3625c710dd3 |
children | 71feabcbe3d2 |
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4:9ff511e32040 | 5:a2d0d346f07c |
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32 <param name="input" value="fa_gc_content_input.fa"/> | 32 <param name="input" value="fa_gc_content_input.fa"/> |
33 <output name="out_file1" file="fa_gc_content_output.txt"/> | 33 <output name="out_file1" file="fa_gc_content_output.txt"/> |
34 </test> | 34 </test> |
35 </tests> | 35 </tests> |
36 <help> | 36 <help> |
37 NSAF Scoring Table | |
38 ^^^^^^^^^^^^^^^^^^ | |
39 | |
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 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 designed as a less stringent alternative to the SaintScore to complement the analysis, functioning as an empirical fold-change. | |
44 | |
45 -------------- | |
46 | |
47 **1) SAINT Output File** | |
48 | |
49 SAINTexpress generated *list.txt* file. | |
50 | |
51 **Note:** Prey IDs must be in Uniprot/Swissprot format (e.g. | |
52 "EGFR\_HUMAN" or "P00533"). | |
53 | |
54 **2) Prey File** | |
55 | |
56 Please specify a *Prey* file for Bubble Graph creation. A *Prey* file | |
57 should contain three columns: prey (protein) name, prey amino acid | |
58 length, and prey gene name. | |
59 | |
60 **3) CRAPome File** | |
61 | |
62 Please specify an *CRAPome* file for Bubble Graph creation. An *Inter* | |
63 file should contain five columns: IP name, Mapped Gene Symbol, Number of | |
64 Experiments (ratio), and Average spectral counts, and Max spectral counts. | |
65 | |
66 **4) Interactions File** | |
67 | |
68 Please specify an *Inter* file for Bubble Graph creation. An *Inter* | |
69 file should contain four columns: IP name, bait name, prey name, and | |
70 spectral counts or intensity values, depending on the mode of | |
71 quantification. | |
72 | |
37 </help> | 73 </help> |
38 </tool> | 74 </tool> |