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Table 2 Quality measures of microarray gene expression values*

From: An optimized workflow for improved gene expression profiling for formalin-fixed, paraffin-embedded tumor samples

  Correlation of gene expression between matched FF and FFPET samples Percentage present call Percentage probe sets with expression > LOB Percentage genes with non-consistent expression across multiple probe sets
Median (25%, 75% quantiles) Median (25%, 75% quantiles)
FF: N/A 49.7 (47.3, 50.6) 51.4 17.4
FFPET: Affymetrix 0.78 (0.72, 0.81) 33.4 (21.8, 38.1) 36.2 19.4
FFPET: NuGEN 0.88 (0.84, 0.89) 47.2 (44.1, 58.1) 52.7 17.9
FFPET: Sigma/Rubicon 0.48 (0.47, 0.52) 22.9 (22.1, 24.6) 16.4 28.0
  1. FF, fresh-frozen; FFPET, formalin-fixed, paraffin-embedded tissue; LOB, limit of blank; N/A, not applicable.
  2. * For the genes represented by at least two probe sets the analysis of consistency of probe set expression is performed. As an overall measure of the consistency we have estimated the percentage of genes for which the Pearson correlation coefficient between expression of all pairs of related probe sets did not exceed 0.5.
  3. As defined by the Affymetrix algorithm.