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IlluminaNormalization

Performs between array normalization for an input matrix. Normalization methods are quantile, ssn (simple scaling normalization), rsn (robust spline normalization), loess, rank invariant and vsn (variance stabilizing normalization). vsn should be directly applied to the raw data, not to the log2/vst transformed data.

The input is a matrix containing ProbeIDs and log2/vst transformed intensity values. First column of the input is the ProbeID followed by columns each representing one array.

The output is a matrix containing ProbeIDs and normalized intensity values. First column of the output is the ProbeID followed by columns each representing one array.

Version 1.0
Bundle microarray
Categories Normalization
Authors Lilli Saarinen (Lilli.Saarinen@Helsinki.FI)
Issue tracker View/Report issues
Requires R ; libxml2-dev (DEB) ; libcurl4-gnutls-dev (DEB) ; lumi (R-bioconductor)
Source files component.xml IlluminaNormalization.r
Usage Example with default values

Inputs

Name Type Mandatory Description
in LogMatrix Mandatory Input matrix of raw data.

Outputs

Name Type Description
out LogMatrix Output matrix of normalized data.

Parameters

Name Type Default Description
method string "quantile" Possible values are "quantile", "ssn", "rsn", "loess", "rankinvariant" and "vsn" normalizations.

Test cases

Test case Parameters IN
in
OUT
out
case1 properties in out

method=quantile

case2 properties in out

method=loess


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