mas5 {affy} | R Documentation

## 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`
`sc` | 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`.

### Details

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

### Value

`ExpressionSet`

The 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/

### See Also

`expresso`,`affy.scalevalue.exprSet`

### Examples

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

[Package affy version 1.65.1 Index]