Tech Notes

Q. Can I view my 2-color data in the form of an M vs. A (MA) plot?

A. Yes. An MA plot can provide insight as to the quality of 2-color array hybridizations. For each data point,



, where R = signal intensity and G = ratio intensity and



A script is available to calculate one list each for the M and A values. Using the scatter plot view, M and A can then be displayed on the vertical and horizontal axis, respectively.

In general, low and even scatter around y=0 is desirable.

To install and use the script in GeneSpring (Version 6)

1. Download the MA plot script
2. Use File -> Import GeneSpring Zip to select the zip file
3. Click once on this script in the Scripts folder
4. Enter the required inputs and click Start.
   
   See the script notes for further explanation of functionality and additional instructions on setting Scatter Plot display options.