This package was produced as part of National Cancer Institute's caBIG project
(https://cabig.nci.nih.gov/) and is also aviable for download from NCI Center 
for Bioinformatics (http://ncicb.nci.nih.gov/download/index.jsp) website as 
well as CRAN (http://cran.r-project.org/) website. 

In current version of R (2.1.1) I expirienced problems with installing the 
package due to inability to find 'PROcess' package, which resides in 
"BioConductor" repository. To make the process smoother one should add 
"BioConductor" to the list of repositories, before the instalation of the 
package. Use "utils::setRepositories()" or "Pakages / Select repositories" 
menu.

See R_home/library/caMassClass/doc for one-page 'road-map' showing how 
functions in this library suppose to interract with each other.

The package was tested on SELDI data produced by:
- Center for Prostate Disease Research (http://www.cpdr.org/) 
- Eastern Virginia Medical School's The Virginia Prostate Center 
  (http://www.evms.edu/vpc/seldi/index.html) 
- NCI's Center for Cancer Research 
  (http://home.ccr.cancer.gov/ncifdaproteomics/ppatterns.asp)

Planned future work on the package include:
- more testing and improvements to classification section of the package
- more examples on real data aviable for download

Other packages related to protiomics mass spectrometry, aviable from CRAN or 
BioConductor websites:
- PROcess - "A package for processing protein mass spectrometry data"
- ppc - "Sample classification of protein mass spectra by peak probabilty 
        contrasts"
- mscalib - "Calibration and filtering methods for calibration of mass 
  spectrometric peptide mass lists. Includes methods for internal, external 
  calibration of mass lists. Provides methods for filtering chemical noise and 
  peptide contaminants."
- RProtiomics - NCI funded project not in form of R packages:
  http://cabigcvs.nci.nih.gov/viewcvs/viewcvs.cgi/rproteomics/

====================================================\==========================                 
 Jarek Tuszynski, PhD.                           o / \ 
 Science Applications International Corporation  <\__,|  
 (703) 676-4192                                   ">   \
 Jaroslaw.W.Tuszynski@saic.com                     `    \

