threestepPLM {affyPLM} | R Documentation

## Three Step expression measures returned as a PLMset

### Description

This function converts an `AffyBatch` into an `PLMset` using a three step expression measure.

### Usage

    threestepPLM(object,subset=NULL, normalize=TRUE, background=TRUE,
                 background.method="RMA.2", normalize.method="quantile",
                 summary.method="median.polish", 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.
`summary.method` | name of summary method to use.
`background.param` | list of parameters for background correction methods
`normalize.param` | list of parameters for normalization methods
`output.param` | list of parameters for output methods
`model.param` | list of parameters for model methods
`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 computes the expression measure using threestep methods. It returns a `PLMset`. The most important difference is that the PLMset allows you to access the residuals which the `threestep` function does not do.

### 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, Berkeley.

### See Also

`expresso`, `rma`, `threestep`, `rmaPLM`, `fitPLM`

### Examples

    if (require(affydata)) {
      data(Dilution)

      # should be equivalent to rma()
      ## Not run: eset <- threestepPLM(Dilution)
    }

[Package affyPLM version 1.68.0 Index]