rma {oligo} | R Documentation

## RMA - Robust Multichip Average algorithm

### Description

Robust Multichip Average methodology. This will convert an (Expression/Exon/Gene)FeatureSet object to an ExpressionSet object by using RMA strategy.

### Usage

    rma(object, ...)

### Arguments

`object` | `FeatureSet` object
`...` | Extra arguments.

### Details

This function computes the RMA (Robust Multichip Average) expression measure described in Irizarry et al Biostatistics (2003).

Note that this expression measure is given to you in log base 2 scale. This differs from most of the other expression measure methods.

For Exon ST and Gene ST arrays, the user should be aware that the summarization is performed to the *probeset* level. The ExpressionSet returned when either Exon/Gene-FeatureSet objects are passed contain extra annotation on the featureData slot that the user should take into account for exon/gene-level analyses.

### Value

`ExpressionSet` object.

### References

Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget Hobbs and Terence P. Speed (2003), Summa ries 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

    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)
    }

[Package oligo version 1.8.3 Index]