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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.

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

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