PathPrint based analysis of gene expression

1) Initial analysis: Preprocessing and normalization of raw data files
(cel files or gct files). Subsequently pathprinted the gene expression
sets (results in results/pathprints posted on
basecamp/[hidelab]/zebraprint)
2) Initial analysis: Initial clustering analysis of experiments to
detect any strong sub-clusters. Preliminary branch-based pathways
extraction of some sub-clusters of interest using nodepathway (Gabriel
Altschuler’s code). (results in results/phylogeny posted on
basecamp/[hidelab]/zebraprint).
3) combat normalization: There were some batch effects confounding
wild-type signals for experiments conducted at the same somite stage.
ComBat normalization was conducted (parametric as well as
non-parametric) to get a better resolution of the mutant vs wildtype
effect in the experiments of interest. (results in
/results/meta_analysis/ComBat normalization analysis)
4) nodepath_geneexprn_BLS.R : meta-analysis conducted to understand
what is driving the difference between samples of interest, at the
pathways (analyzing the nodes), and at the gene (differential
expression) level.
Revert "PathPrint based analysis of gene expression"

This reverts commit a0b000e22fb09502dab49e359ef687475f710043.
Merge branch 'master' of https://github.com/jasgrewal/zebraprint