Table 2.

Correlation coefficients between gene expression measured for different dyes at various laser settings for the cDNA array. Correlation coefficients for all genes on the PHASE-I cDNA array between combinations of dyes at different scanner settings for 1 array, and at laser power 100 settings for 5 arrays.

	array1			laser power = 100 (n = 5)
Settings	laser = 70	original settings	laser = 100	mean ± stdev
Dye combination
Alexa 488 vs Alexa 594	0.953	0.967	0.965	0.953 ± 0.020
Alexa 488 vs Alexa Cy3	0.916	0.941	0.955	0.923 ± 0.044
Alexa 488 vs Cy5	0.890	0.935	0.935	0.942 ± 0.014
Alexa 594 vs Cy3	0.958	0.983	0.988	0.938 ± 0.053
Alexa 594 vs Cy5	0.946	0.978	0.979	0.986* ± 0.005
Cy3 vs Cy5	0.975	0.981	0.987	0.926* ± 0.062
Mean	0.940	0.964	0.968	0.945 ± 0.025

Original scanner settings for Alexa 488, Alexa 594, Cy3 and Cy5 are: laser power 93, 91, 89 and 80% respectively, and PMT Gain 72, 71, 91, 60% respectively.

* The correlation coefficient between Alexa 594 – Cy5 is significantly higher than the correlation coefficient for any dye combination with Alexa 488, and the combination Alexa 594-Cy3 has a significantly higher correlation coefficient than Cy3-Cy5 (t-test, p < 0.05).