rma-methods: RMA - Robust Multichip Average algorithm

Description Usage Arguments Methods References See Also Examples

Description

Robust Multichip Average preprocessing methodology. This strategy allows background subtraction, quantile normalization and summarization (via median-polish).

Usage

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  ## S4 method for signature 'ExonFeatureSet'
rma(object, background=TRUE, normalize=TRUE, subset=NULL, target="core")
  ## S4 method for signature 'HTAFeatureSet'
rma(object, background=TRUE, normalize=TRUE, subset=NULL, target="core")
  ## S4 method for signature 'ExpressionFeatureSet'
rma(object, background=TRUE, normalize=TRUE, subset=NULL)
  ## S4 method for signature 'GeneFeatureSet'
rma(object, background=TRUE, normalize=TRUE, subset=NULL, target="core")
  ## S4 method for signature 'SnpCnvFeatureSet'
rma(object, background=TRUE, normalize=TRUE, subset=NULL)

Arguments

object

Exon/HTA/Expression/Gene/SnpCnv-FeatureSet object.

background

Logical - perform RMA background correction?

normalize

Logical - perform quantile normalization?

subset

To be implemented.

target

Level of summarization (only for Exon/Gene arrays)

Methods

signature(object = "ExonFeatureSet")

When applied to an ExonFeatureSet object, rma can produce summaries at different levels: probeset (as defined in the PGF), core genes (as defined in the core.mps file), full genes (as defined in the full.mps file) or extended genes (as defined in the extended.mps file). To determine the level for summarization, use the target argument.

signature(object = "ExpressionFeatureSet")

When used on an ExpressionFeatureSet object, rma produces summaries at the probeset level (as defined in the CDF or NDF files, depending on the manufacturer).

signature(object = "GeneFeatureSet")

When applied to a GeneFeatureSet object, rma can produce summaries at different levels: probeset (as defined in the PGF) and 'core genes' (as defined in the core.mps file). To determine the level for summarization, use the target argument.

signature(object = "HTAFeatureSet")

When applied to a HTAFeatureSet object, rma can produce summaries at different levels: probeset (as defined in the PGF) and 'core genes' (as defined in the core.mps file). To determine the level for summarization, use the target argument.

signature(object = "SnpCnvFeatureSet")

If used on a SnpCnvFeatureSet object (ie., SNP 5.0 or SNP 6.0 arrays), rma will produce summaries for the CNV probes. Note that this is an experimental feature for internal (and quick) assessment of CNV probes. We recommend the use of the 'crlmm' package, which contains a Copy Number tool specifically designed for these data.

References

Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget Hobbs and Terence P. Speed (2003), Summaries of Affymetrix GeneChip probe level data Nucleic Acids Research 31(4):e15

Bolstad, B.M., Irizarry R. A., Astrand M., and Speed, T.P. (2003), A Comparison of Normalization Methods for High Density O ligonucleotide Array Data Based on Bias and Variance. Bioinformatics 19(2):185-193

Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis, KJ, Scherf, U, Speed, TP (2003) Exploration, Normalizati on, and Summaries of High Density Oligonucleotide Array Probe Level Data. Biostatistics. Vol. 4, Number 2: 249-264

See Also

snprma

Examples

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if (require(maqcExpression4plex) & require(pd.hg18.60mer.expr)){
xysPath <- system.file("extdata", package="maqcExpression4plex")
xysFiles <- list.xysfiles(xysPath, full.name=TRUE)
ngsExpressionFeatureSet <- read.xysfiles(xysFiles)
summarized <- rma(ngsExpressionFeatureSet)
show(summarized)
}

Bioconductor-mirror/oligo documentation built on July 28, 2017, 5:23 a.m.