Merge with 9d2f7886d46acc8d1d7539ef0c4f3e1c59294569
Small bugfixes to various microarray tools, updated manual page for GEO import.
Small bugfix to two aCGH scripts.
Migrating copy number tools from R 2.12 to 2.15.
Merge with 31f148f50aad684ce4f7da80fab072e883e9fe12
merge
Adding aCGH tools to CNA-seq.
Copied acgh-segment.R to cna-segment.R. These two will diverge in the future.
Added a new aCGH tool.
Fixed too search-coordinates.R and added it to microarray-module.xml
Updates to copy number tools.
Changes to CNA-seq tools.
Added manual page for the normalization tool for copy number data.
Copy number updates.
Changed copy number scripts using runtime R-2.15 to R-2.15_bioc-2.11, and removed old R-2.12 versions.
Updates to copy number tools.
Copy number updates.
Added .gitignore, removed CVS stuff.
Corrected typo in acgh-convert-from-probes-to-genes.R
Merge branch 'master' into chipster-2.0_scripts

Conflicts:
	.gitignore
	src/main/modules/microarray/R-2.12/qc-cdna.R
	src/main/modules/microarray/R-2.12/stat-two-groups.R