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Table 3 Average Spearman's correlations between MA and qRT-PCR detection of differentially expressed genes

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

   MAS5 PLIER MBEImm GC-RMA RMA MBEI
new annotation A 71 ± 19 77 ± 9 80 ± 14 82 ± 9 74 ± 17 71 ± 15
  N 71 ± 19 77 ± 9 81 ± 14 82 ± 9 74 ± 17 71 ± 15
  D 74 ± 8 73 ± 15 82 ± 10 82 ± 8 75 ± 13 70 ± 13
  F 73 ± 20 83 ± 9 81 ± 13 84 ± 10 79 ± 19 79 ± 13
  FN 73 ± 20 83 ± 10 81 ± 14 84 ± 10 79 ± 19 79 ± 13
  FD 75 ± 15 77 ± 15 84 ± 13 80 ± 11 77 ± 16 74 ± 10
old annotation A 70 ± 20 76 ± 11 78 ± 16 81 ± 12 76 ± 14 70 ± 15
  N 70 ± 21 77 ± 11 79 ± 15 80 ± 14 76 ± 15 72 ± 15
  D 75 ± 8 74 ± 14 82 ± 11 74 ± 14 74 ± 14 69 ± 15
  F 72 ± 22 82 ± 10 78 ± 15 81 ± 13 79 ± 14 78 ± 16
  FN 72 ± 22 83 ± 9 79 ± 14 81 ± 15 79 ± 15 80 ± 15
  FD 77 ± 13 77 ± 15 84 ± 14 77 ± 16 77 ± 16 71 ± 13
  1. The table contains mean values and the corresponding standard deviations of Spearman's correlation coefficients calculated for 6 experiments. Correlations were computed between values of Welch's t-statistic 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.