MA-plots
MA-plots are used to study dependences between the log ratio of two variables and the mean values of the same two variables. The log ratios of the two measurements are called M values (from “minus” in the log scale) and are represented in the vertical axis. The mean values of the two measurements are called A values (from “average” in the log scale) and are represented in the horizontal axis.
In microarray data contexts an MA-plot is used to compare two channels of intensity measurements. These two channels can be the red and green channels of one single chip of a two-color platform or the intensity measurements of two different arrays when using a single-channel platform. In a single-channel context at least two arrays are needed to draw a meaningful MA-plot.
References:
Yang,Y.H., Dudoit,S., Luu,P., Lin,D.M., Peng,V., Ngai,J. and Speed,T.P. (2002) Normalization for CDNA microarray data: a robust composite method addressing single and multiple slide systhematic variation. Nucleic Acids Res., Vol.30, No.4, e15.
Bolstad, B. M., Irizarry, R. A., Astrand, M., Speed TP (2003). A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193.