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Table 2 Percentage of genes identical among all genes detected by different combinations of normalization and statistical analysis

From: Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis

  Invariant feature; AD, F Invariant feature; AD, KW Invariant feature; AD, SAM Invariant feature; MBEV, F Invariant feature; MBEV, KW Invariant feature; MBEV, SAM Invariant set; F Invariant set; KW Invariant set; SAM Global scaling; F Global scaling; KW Global scaling; SAM
Invariant feature; AD, F   93 100 78 83 92 81 83 88 64 74 78
Invariant feature; AD, KW 74   95 67 79 82 74 79 81 55 67 69
Invariant feature; AD, SAM 56 66   51 59 74 58 61 66 41 50 54
Invariant feature; MBEV, F 69 75 82   96 100 77 80 82 58 67 70
Invariant feature; MBEV, KW 62 74 79 80   95 71 75 77 51 62 64
Invariant feature; MBEV, SAM 56 63 81 68 77   63 66 70 44 53 57
Invariant set; F 59 69 77 63 70 76   98 100 56 67 70
Invariant set; KW 56 67 74 60 68 74 90   96 52 66 66
Invariant set; SAM 55 64 74 58 65 73 85 89   49 61 66
Global scaling; F 80 87 92 81 86 90 95* 96* 98*   100 100
Global scaling; KW 72 83 88 73 82 85 89 96* 95* 78   93
Global scaling; SAM 70 78 88 71 77 84 85 89 94* 72 86  
  1. Percentages are relative to the method defined in the column headings. Values of 100% and greater than 90% are highlighted in bold. *Percentage of genes identified after invariant probe set normalization that are also identified after global scaling (see text for details).