Skip to main content

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.