[BioC] quality assessment of microarray using arrayQualityMetrics

[Amit]

Dear All,

I am working on large dataset of two color arrays. For two color
arrays the normalizeBetweenArray function (limma) produces MAList from
RGList after normalization. My question is after normalization of two
color microarray data, whether arrayQualityMetrics should be run on M
(log ratios) matrix or A (average log intensity) matrix ? I am
guessing it should be run on A matrix as arrayQualityMetrics requires
matrix of microarray intensities to perform the analysis. But, I am
not sure. Any suggestion is appreciated.

regards
Amit