rmaPLM {affyPLM} | R Documentation

## Fit a RMA to Affymetrix Genechip Data as a PLMset

### Description

This function converts an `AffyBatch` into an `PLMset` by fitting a multichip model. In particular we concentrate on the RMA model.

### Usage

    rmaPLM(object, subset=NULL, normalize=TRUE, background=TRUE,
           background.method="RMA.2", normalize.method="quantile",
           background.param=list(), normalize.param=list(), output.param=list(),
           model.param=list(), verbosity.level=0)

### Arguments

`object` | an `AffyBatch`
`subset` | a vector with the names of probesets to be used. If NULL then all probesets are used.
`normalize` | logical value. If `TRUE` normalize data using quantile normalization
`background` | logical value. If `TRUE` background correct using RMA background correction
`background.method` | name of background method to use.
`normalize.method` | name of normalization method to use.
`background.param` | A list of parameters for background routines
`normalize.param` | A list of parameters for normalization routines
`output.param` | A list of parameters controlling optional output from the routine.
`model.param` | A list of parameters controlling model procedure
`verbosity.level` | An integer specifying how much to print out. Higher values indicate more verbose. A value of 0 will print nothing

### Details

This function fits the RMA as a Probe Level Linear models to all the probesets in an `AffyBatch`.

### Value

An `PLMset`

### Author(s)

Ben Bolstad bmb@bmbolstad.com

### References

Bolstad, BM (2004) Low Level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization. PhD Dissertation. University of California,
Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B and Speed TP (2003) Summaries of Affymetrix GeneChip probe level data Nucleic Acids Research 31(4):e15
Bolstad, BM, Irizarry RA, Astrand, M, and Speed, TP (2003) A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics 19(2):185-193

### See Also

`expresso`, `rma`, `threestep`,`fitPLM`, `threestepPLM`

### Examples

    if (require(affydata)) {
      # A larger example testing weight image function
      data(Dilution)
      ## Not run: Pset <- rmaPLM(Dilution,output.param=list(weights=TRUE))
      ## Not run: image(Pset)
    }

[Package affyPLM version 1.62.0 Index]