minfi (version 1.18.4)

preprocessIllumina: Perform preprocessing as Genome Studio.

Description

These functions implements preprocessing for Illumina methylation microarrays as used in Genome Studio, the standard software provided by Illumina.

Usage

preprocessIllumina(rgSet, bg.correct = TRUE, normalize = c("controls", "no"), reference = 1)
bgcorrect.illumina(rgSet)
normalize.illumina.control(rgSet, reference = 1)

Arguments

rgSet

An object of class RGChannelSet.

bg.correct

logical, should background correction be performed?

normalize

logical, should (control) normalization be performed?

reference

for control normalization, which array is the reference?

Value

preprocessIllumina returns a MethylSet, while bgcorrect.illumina and normalize.illumina.control both return a RGChannelSet with corrected color channels.

Details

We have reverse engineered the preprocessing methods from Genome Studio, based on the documentation.

The current implementation of control normalization is equal to what Genome Studio provides (this statement is based on comparing Genome Studio output to the output of this function), with the following caveat: this kind of normalization requires the selection of a reference array. It is unclear how Genome Studio selects the reference array, but we allow for the manual specification of this parameter.

The current implementation of background correction is roughly equal to Genome Studio. Based on examining the output of 24 arrays, we are able to exactly recreate 18 out of the 24. The remaining 6 arrays had a max discrepancy in the Red and/or Green channel of 1-4 (this is on the unlogged intensity scale, so 4 is very small).

A script for doing this comparison may be found in the scripts directory (although it is of limited use without the data files).

See Also

RGChannelSet and MethylSet as well as IlluminaMethylationManifest for the basic classes involved in these functions. preprocessRaw is another basic preprocessing function.

Examples

if (require(minfiData)) {

dat <- preprocessIllumina(RGsetEx, bg.correct=FALSE, normalize="controls")
slot(name="preprocessMethod", dat)[1]

}