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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]