Scripts for normalization and analysis of Illumina methylation array data.

Requires recent Java and ANT. To compile, type:

   ant

Then add metharray.jar, bjv2-core-0.1.jar and colt.jar to your CLASSPATH

These scripts expect data as tab-delimited matrices with a probe ID in the first column and numerical values in all other columns. You can add some header lines (starting with '#') if you like.

Normalization

   java data.t1d.MatrixQuantileApplication matrix.txt >matrix.qn.txt

Calling differences

Samples are divided into "foreground" (treatment, mutant, affected, whatever) and "background" (controls, normals). They are identified by zero-based column indices.

   java data.t1d.PairwiseDMRCallerWApplication -fg 1,3,5 -bg 2,4,6 matrix.qn.txt >dmrcalls.txt

P-values are in column 3 of the output file.