R30 updates to microarray packages
bugs in ROST corrected
Merge branch 'master' into R30
more R3 updates
design-mat analysis removed
R30 changes to illumina normalisation script
Cluster scripts changed to R3
HTML Annotation modified to include full original table
stat-geneset updated to R30
Bugs fixed in stat-geneset.R
Pathway tools moved to R-3
BAM input for FastQC, R3.0 testing
fastqc manual
Pathway tools moved to R3
Merge branch 'master' into R30

Conflicts:
	src/main/modules/microarray/R-2.12/pathways-mirna-hyperg-go.R
	src/main/modules/microarray/microarray-module.xml
	src/main/modules/ngs/R-2.12/ngs-filter-annotations.R
Deleted duplicated pathways-mirna-hyperg-go scripts
Merge branch 'r3testing' into R30
Kimmo's & Ari-Matti's changes merged to R3
Merge branch 'master' into R30
Merge branch 'master' into R30