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Table 1 Statistical analyses involved in the seven different methods for calculating gene expression.

From: Methods for evaluating gene expression from Affymetrix microarray datasets

Methods Background Correction Normalization Core Statistical Analysis References
AD None Invariant Set Average difference Affymetrix [2]
MAS5.0 Spatial effect and MM subtracted Constant Robust average (Tukey bi-weight) Affymetrix [2]
MBEI (PM only) None Invariant Set Multiplicative model Li and Wong [5]
MBEI (PM-MM) MM intensities are subtracted Invariant Set Multiplicative model Li and Wong [5]
RMA Global correction Quantile Robust linear model (median polish) Irizarry et al. [4]
PDNN Model is fitted accounting for background and specific signal Quantile Specific and non-specific binding effects are estimated using free energy model Zhang et al. [7]
GCRMA Based on probe sequence Quantile Robust linear model (median polish) Wu et al. [8]