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Table 3 Statistical comparison of normalization schemes

From: Model selection and efficiency testing for normalization of cDNA microarray data

  Experiment No normalization Linear normalization Global lowess P-lowess S-lowess LIN OLIN OSLIN
Intensity-dependent cor(M, ) SW480/620 0.50 0.50 0.01 -0.01 -0.01 0.04 0.00 0.00
Intensity-dependent cor(M, ) Apo AI 0.47 0.47 0.06 0.05 0.05 0.09 0.00 0.00
Spatial cor(M, ) SW480/620 0.53 0.53 0.56 0.34 0.32 0.27 0.07 0.08
Spatial cor(M, ) Apo AI 0.58 0.58 0.59 0.41 0.38 0.43 0.15 0.15
Mean pairwise cor(M) SW480/620 0.46 0.46 0.50 0.59 0.59 0.63 0.67 0.64
Var(M) SW480/620 927.1 658.7 455.4 216.3 213.0 205.7 163.0 186.5
Number of significant genes SW480/620 26 71 51 75 88 94 99 129
Average cor(MqPCR, Mma) Fibroblast 0.82 0.81 0.82 0.82 0.81 0.81 0.84 0.88
  1. Intensity-dependent correlation (intensity-dependent cor(M, )) describes the correlation between the log ratio M of the spot and the median value of M within a symmetrical neighborhood of 50 spots on the intensity scale. Spatial correlation (spatial cor(M, )) describes the correlation between the log ratio M of the spot and the median value of M within a neighborhood defined by a window of 5 × 5 spots. To ensure independence, M of the spot was not included in the median of the neighborhood. For the calculation of mean pairwise correlation of slides, spots with intensity A < 11.6 were excluded. The significance of differential gene expression was examined by a one-sample t-test with the null hypothesis of mean log ratio M = 0. Duplicated spots on SW480/620 arrays were treated as independent measurements producing a maximum of eight observations per gene. Genes were detected as significantly differentially expressed if their Bonferroni adjusted p-values were smaller than 0.01. For the fibroblast experiment, the average Pearson correlation between qPCR-based logged fold changes M qPCR and microarray-based logged fold changes M ma of the genes for IL-8, COX2, Mast, B4-2 and actin is shown.