Mercurial > repos > bornea > nsaf_scoring
changeset 7:71feabcbe3d2 draft
Uploaded
| author | bornea |
|---|---|
| date | Tue, 17 May 2016 13:01:01 -0400 |
| parents | 5f09f5eeda75 |
| children | f59b4984a974 |
| files | nsaf_scoring.xml |
| diffstat | 1 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/nsaf_scoring.xml Wed May 11 12:52:57 2016 -0400 +++ b/nsaf_scoring.xml Tue May 17 13:01:01 2016 -0400 @@ -36,12 +36,16 @@ <help> NSAF Scoring Table ^^^^^^^^^^^^^^^^^^ +This tool is a static version of the APOSTL interactive affinity proteomics analysis software that calculates the NSAF, NSAF Score, and optionally the CRAPomePCT. -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 +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. +CRAPomePCT is the probability of a true interaction based on the abundance of a protein in the CRAPome database. + +APOSTL was developed at H. Lee Moffitt Cancer Center and Research Institute and distributed under a GNU General Public License (GPL). -------------- **1) SAINT Output File** @@ -59,7 +63,7 @@ **3) CRAPome File** -Please specify an *CRAPome* file for Bubble Graph creation. An *Inter* +Please specify an *CRAPome* file for Bubble Graph creation. An *CRAPome* file should contain five columns: IP name, Mapped Gene Symbol, Number of Experiments (ratio), and Average spectral counts, and Max spectral counts.