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

BMC Bioinformatics

Table 1 Summary of EzArray microarray data preprocessing methods

*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

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.

ISSN: 1471-2105