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Table 3 Correlation of platform data and sample-matched QRT-PCR data

From: Comparison of the latest commercial short and long oligonucleotide microarray technologies

  

Log2-ratio vs. -ΔΔCT

log2-int vs. -ΔCT

  

Pearson

p

Spearman

p

Pearson

p

Spearman

p

AFFYMETRIX

med

0.91

0.001

0.87

0.017

0.79

0.031

0.84

0.016

 

max

1

 

0.97

 

0.93

 

0.97

 

AMERSHAM

med

0.72

0.105

0.54

0.297

0.77

0.029

0.9

0.027

 

max

0.92

 

0.88

 

1

 

1

 

AGILENT

med

0.92

0.039

0.76

0.208

    
 

max

1

 

1

     
  1. Shown are median (med) and maximum (max) Pearson and Spearman rank correlation coefficients calculated from all pair-wise combinations between all replicate arrays and for all cell lines. The median p values (p) from all of the tests are also shown. We are presenting 2 types of comparisons depending on the type transformation used: log2-ratios platform data versus (vs.) -ΔΔCt QRT-PCR data; and log2-intensities (for the one-color platforms) versus -ΔCt QRT-PCR data. Only array data points for 12 out of the 14 genes that were available for all platforms were included in the calculations.
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BMC Genomics

ISSN: 1471-2164

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