Miscellaneous copy number updates

A few updates to the copy number scripts( and quality control tools for Agilent 2-color and cDNA (which by the way are the exact same tool, just with two different names)).

The most important is the change from vector to raster images in the PDF file generated by acgh-plot-profile.R. With vector images the file sizes grew so big that the pdf library Chipster uses caused it to run out of memory quite easily with bigger data sets. Now this shouldn't happen. It requires installation of the 'png' library for R-2.15_bioc-2.11 (it's in CRAN).