Table 3. Overlapping probe sets produce more consistent difference calls between Affymetrix and Agilent cDNA microarray platforms.

Platform	Type	t-value	P-value	Cramer’s coefficient
133A	Overlapping	3805	<0.001	0.18
	Non-overlapping	511	<0.001	0.07
95A	Overlapping	3702	<0.001	0.24
	Non-overlapping	160	<0.001	0.06
133B	Overlapping	478	<0.001	0.18
	Non-overlapping	80	<0.001	0.04

Difference calls were calculated for RNA samples comparing MDA-MB-436 cells to the HMEC cells and comparing the HCC1954 cells to the HMEC cells using the manufacturer’s algorithm for both platform types. Only consistent calls between duplicate measurements were included in the analysis. t-Values and Cramer coefficients were calculated as described in the text for 3 × 3 contingency tables.