Table 3.

Correlation of platform data and sample-matched QRT-PCR data

		Log2-ratio vs. -ΔΔCT				log2-int vs. -ΔCT
		Pearson	p	Spearman	p	Pearson	p	Spearman	p
AFFYMETRIX	med	0.91	0.001	0.87	0.017	0.79	0.031	0.84	0.016
	max	1		0.97		0.93		0.97
AMERSHAM	med	0.72	0.105	0.54	0.297	0.77	0.029	0.9	0.027
	max	0.92		0.88		1		1
AGILENT	med	0.92	0.039	0.76	0.208
	max	1		1

Shown are median (med) and maximum (max) Pearson and Spearman rank correlation coefficients calculated from all pair-wise combinations between all replicate arrays and for all cell lines. The median p values (p) from all of the tests are also shown. We are presenting 2 types of comparisons depending on the type transformation used: log₂-ratios platform data versus (vs.) -ΔΔCt QRT-PCR data; and log₂-intensities (for the one-color platforms) versus -ΔCt QRT-PCR data. Only array data points for 12 out of the 14 genes that were available for all platforms were included in the calculations.