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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.

From: Application of four dyes in gene expression analyses by microarrays

  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
  1. 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.
  2. * 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).