... dye-swap design can be characterized by a standard design matrix Z with rows for each array channel and columns for the comparison groups, dyes, and arrays Specifically, with n arrays and p comparison ... groups The fANOVA model and its basis matrix representation allow for flexible choices of the form of its component functions, as well as for the inclusion of additional sources of bias The dye functions ... channel normalization, models of variations and assessment of gene effects Nucleic Acids Res 2001, 29:2540-2557 Yang YH, Dudoit S, Luu P, Speed TP: Normalization of cDNA microarrays In Microarrays: ...