README
    ComputeDissimilarityJK-queryStudy.pl - main script
    ComputeStudyDissMatrix.pl - perl script to calculate dissimilarity 
      measures between a pair of experiments
    Dissimilarities.pm - an utils package for dissimilarity calculations
    mage2matrix.pl - a perl script to extract annotations from a MAGE-TAB
      (IDF, SDRF) file
    cluster-sil.R-v2.7 - R script to perform clustering analysis, 
      compatible with R version 2.7
    cluster-sil.R-v2.9 - R script to perform clustering analysis, 
      compatible with R version 2.9
 
RELEASE DATE
    September 10, 2010
    
RELEASE VERSION
    

DESCRIPTION

ComputeDissimilarityJK-queryStudy.pl is the main script to query a set
of experiments with an example experiment and return the experiments ranked 
by decreasing similarity scores with the query one.    
This script uses Dissimilarities.pm. 

mage2matrix.pl is used to extract annotations from a MAGE-TAB file into the 
format required by the ComputeStudyDissMatrix.pl and 
ComputeDissimilarityJK-queryStudy.pl perl scripts.

ComputeStudyDissMatrix.pl is the script to compute the dissimilarity measures
between a pair of experiments and generate dissimilarity matrix required by 
R scripts


PREREQUISITES

Error.pm are required. Test::Unit is optional if you want to run
the unit test scripts inside the distributed package. 
The CPAN module Statistics::Descriptive is also a requirement.
R version 2.7 or 2.9 are required. 

INSTALLATION

1. Download
http://www.cbil.upenn.edu/downloads/AnnotationCompute/Dissimilarities.pm
and place it in a subdirectory named 'AnnotCompute'.

2. Download Perl and R scripts under
http://www.cbil.upenn.edu/downloads/AnnotationCompute/
      
RUN THEM

1. mage2matrix.pl, ComputeDissimilarityJK-queryStudy.pl and ComputeStudyDissMatrix.pl have 
   perlpod documentation embedded. 
   Run pod2html on this script to get an HTML documentation file.
2. R scripts contain all the detail comments. Run it like this:
   R --slave --no-save --args inFilename=matrixFile groupNum=3 outResFilename=outFile.res 
   outIdFilename=outFile.ids  <cluster-sil.R-v2.7

AUTHORS

    Junmin Liu (junmin@pcbi.upenn.edu)
    Elisabetta Manduchi (manduchi@pcbi.upenn.edu)
    Julia Stoyanovich (jstoy@seas.upenn.edu)
    Chris Stoeckert (stoeckrt@pcbi.upenn.edu)	
    Jie Zheng (jiezheng@pcbi.upenn.edu)

Copyright (c) 2008 The Computational Biology and Informatics Laboratory (CBIL) at the 
University of Pennsylvania. All rights reserved.