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Table 1 Summary of EzArray microarray data preprocessing methods

From: EzArray: A web-based highly automated Affymetrix expression array data management and analysis system

Methods Background Correction Normalization PM correction Summarization
RMA rma quantiles pmonly medianpolish
MAS5 mas mas mas mas
dChip   invariantset pmonly liwong
GCRMA gcrma quantiles pmonly medianpolish
Custom Methods: rma rma2 mas gcrma-eb gcrma-mle quantiles quantiles.robust loess contrast constant invariantset qspline vsn pmonly mas subtractmm medianpolish avdiff liwong mas playerout rlm
  1. The predefined methods RMA, MAS5, and GCRMA are named mainly based on the background correction algorithms, while dChip is named based the unique summarization algorithm. Custom method allows users to specify algorithms for background correction, normalization, PM correction, and summarization. Please review references [15, 16, 33, 34] and references therein for descriptions of these algorithms and comparisons among them.