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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).