Automated Processing of High-resolution Intensity Data
Copyright © 2007 Richard J. Edwards - See source code for GNU License Notice
This modules takes for input the partially processed results of MS analysis, with intensity data, filters based on scores thresholds, removes redundancy (using PINGU) and calculates relative intensity scores. PINGU is then used to generate outputs for use with Cytoscape and other visualisation tools.
Input takes the form of a delimited text file with the following column headers: Expt, Subpop, Identifier, logInt, Score. In addition, other columns may be present (and may be used to filter data). The "unique" column headers allow individual identifications to be isolated, which is important for data filtering and intensity mapping.
Intensities are converted into relative intensities with two options: (1) the redundancy level determines which results are combined. This may be simply at the identified peptide level, the gene level, or even at the protein family level (as determined through BLAST homology). If "fam" is used then GABLAM will be used to generate families for a given level of identity.
**Note.** Core functionality has not been checked/developed since 2010.
Intensity Combination Options
History Module Version History
# 0.0 - Initial Compilation. # 0.1 - Added fam NR using GABLAM and SLiMCore. # 0.2 - Added replicates and pepnum abundance. # 0.3 - Improvements incorporating GeneMap version of Pingu. # 0.4 - Allowed mutliple runs from one call. Added fullmonty option. Moved and corrected compare mode. # 1.0 - Full initial working version. # 1.1 - Added PNG visualisations. # 1.2 - Added additional filtering according to replicate counts (minrep=X). # 1.3 - Added additional filtering according to min peptide occurrences (minpep=X,Y) # 2.0 - Reduced options and tidied code substantially with additional intermediate data outputs. # 2.1 - Reduced import commands. # 2.2 - Updated for revised SLiMCore.
© 2015 RJ Edwards. Contact: firstname.lastname@example.org.