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Normalization

Parent category Preprocessing
Description Different normalization components and methods
Component Version Inputs Outputs Description
ACGHnorm 1.4 caseIn, control, admixtureMatrix, probeAnnotation casechannel, controlchannel, fit Normalizes two channel array CGH data with LOESS, median or mode.
AffyNormalization 1.0 affy, sampleNames report Reads in Affymetrix gene expression microarrays and compares various normalization methods.
HTSeqExprNormalize 0.1 expr array Takes as input "raw", integer count expression matrix of quantified sequenced reads and outputs a scale-normalised, log-transformed expression matrix.
IlluminaNormalization 1.0 in out Performs between array normalization for an input matrix.
LimmaNormalizer 0.6 green, greenBG, red, redBG, groups logratio Normalizes two-channel and single-channel microarrays using the Bioconductor Limma package.
LinearNormalizer 1.0 in out Normalizes the input matrix column-wise.

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