Table 3.

Correlation coefficients between gene expression measured for different dyes at various laser settings for the oligonucleotide array. Correlation coefficients for all genes on the oligonucleotide array between combinations of dyes at different scanner on 1 array, and at laser power 100 settings for 7 arrays. Alexa 488 labelled samples were only hybridized on the first array.

	array1		laser power = 100 (n = 7)
Settings	laser = 70	laser = 100	mean ± stdev
Dye combination
Alexa 488 vs Alexa 594	0.118	0.561
Alexa 488 vs Alexa Cy3	0.080	0.512
Alexa 488 vs Cy5	0.127	0.486
Alexa 594 vs Cy3	0.334	0.857	0.855 ± 0.032
Alexa 594 vs Cy5	0.279	0.808	0.853 ± 0.027
Cy3 vs Cy5	0.313	0.887	0.890* ± 0.052
Mean	0.208	0.685	0.843 ± 0.072

* The correlation coefficient between Cy3 – Cy5 is significantly higher than the correlation coefficient of Alexa 594 – Cy3 (t-test, p < 0.05).