Using NMcl2tab

It is possible to perform the normalization of the tiling arrays at the same time than the extraction from the .CEL files. The program NMcl2tab proposes 3 types of quantile-based normalization procedure:

• qq: quantile normalization,
• lqq: log2 transformation followed by quantile normalization,
• qql: quantile normalization followed by log2 transformation.

So, suppose we want to quantile normalize the previous arrays using the qql procedure. We can then do that by using the -n short option as follows:

$ NMcl2tab -c Data/BY_S288c/Array/NucOccupancy.conf \
           -d Data/BY_S288c/Array/ -p S1/BY_S288c/BY_S288c.prb \
           -o Data/BY_S288c/Array/NucOccupancy_raw.txt
           -n qql