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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.