[BioC] snapCGH: log2ratio

[caiwei at mdanderson.org]

Dear list,

Are the Log2 ratios in our MAlist the log ratios of test sample/reference
sample? or the log ratios of Cy5/Cy3 as when we run normalizeWithinArrays
in Limma?  I am confused when I read the section of  "Reading Data" about
the design vector .

Thanks,

Caimiao