Skip to main content

Table 4 Average Pearson's correlations between MA and qRT-PCR for estimation of the fold change

From: Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements

   MAS5 PLIER MBEImm GC-RMA RMA MBEI
new annotation A 86 ± 11 86 ± 10 89 ± 10 84 ± 9 82 ± 14 81 ± 13
  N 86 ± 11 86 ± 10 89 ± 10 85 ± 10 82 ± 14 81 ± 13
  D 88 ± 9 86 ± 10 88 ± 10 85 ± 7 86 ± 9 81 ± 14
  F 88 ± 11 92 ± 8 90 ± 10 89 ± 10 85 ± 15 85 ± 14
  FN 88 ± 11 92 ± 8 90 ± 10 90 ± 10 85 ± 15 85 ± 14
  FD 90 ± 9 90 ± 9 91 ± 11 89 ± 6 88 ± 9 84 ± 15
old annotation A 84 ± 13 84 ± 11 88 ± 12 82 ± 11 82 ± 13 79 ± 15
  N 85 ± 13 86 ± 11 89 ± 10 84 ± 11 84 ± 11 81 ± 13
  D 88 ± 9 85 ± 10 86 ± 11 87 ± 9 87 ± 9 80 ± 14
  F 85 ± 13 89 ± 11 88 ± 12 87 ± 13 85 ± 14 83 ± 17
  FN 87 ± 13 91 ± 10 90 ± 10 89 ± 11 87 ± 12 85 ± 14
  FD 90 ± 9 90 ± 9 90 ± 12 88 ± 9 88 ± 9 84 ± 16
  1. The table contains mean values and the corresponding standard deviations of Pearson's correlation coefficients. Correlations were computed between fold changes calculated from MA and qRT-PCR measurements. Columns contain results for the 6 preprocessing algorithms, whereas rows contain results for the 6 filtering/mapping methods (negative signs are removed and values are multiplied by 100) after the new and the old annotations.