MA plot

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MA plots are used to visualize intensity-dependent ratio of raw microarray data. The MA plot uses M as the y-axis and A as the x-axis where M and A are usually defined as:

\textstyle{M=log_2 R - log_2 G} 
\textstyle{A=\frac12 \times (log_2 R + log_2 G)}

The MA plot gives a quick overview of the data.

In many microarray gene expression experiments, the general assumption is that most of the genes would not see any change in their expression. Therefore the majority of the points on the y axis(M) would be located at 0, since Log(1) is 0.

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M is, therefore, the intensity ratio and A is the average intensity for a dot in the plot.