mas5: MAS 5.0 expression measure

Description

This function converts an instance of AffyBatch into an instance of ExpressionSet using our implementation of Affymetrix's MAS 5.0 expression measure.

Usage

mas5(object, normalize = TRUE, sc = 500, analysis = "absolute", ...)

Arguments

object

an instance of AffyBatch

normalize

logical. If TRUE scale normalization is used after we obtain an instance of ExpressionSet

Value at which all arrays will be scaled to.

analysis

should we do absolute or comparison analysis, although "comparison" is still not implemented.

...

other arguments to be passed to expresso.

Value

ExpressionSetThe methods used by this function were implemented based upon available documentation. In particular a useful reference is Statistical Algorithms Description Document by Affymetrix. Our implementation is based on what is written in the documentation and, as you might appreciate, there are places where the documentation is less than clear. This function does not give exactly the same results. All source code of our implementation is available. You are free to read it and suggest fixes.For more information visit this URL: http://stat-www.berkeley.edu/users/bolstad/

Details

This function is a wrapper for expresso and affy.scalevalue.exprSet.

Examples

Run this code

if (require(affydata)) {
  data(Dilution)
  eset <- mas5(Dilution)
}