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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).
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BMC Genomics

ISSN: 1471-2164

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