mas4 {xps} | R Documentation

## MAS 4.0 Expression Measure

### Description

This function converts a `DataTreeSet` into an `ExprTreeSet` using the XPS implementation of Affymetrix's MAS 4.0 expression measure.

### Usage

    mas4(xps.data,
         filename   = character(0),
         filedir    = getwd(),
         tmpdir     = "",
         normalize  = FALSE,
         sc         = 500,
         option     = "transcript",
         exonlevel  = "",
         update     = FALSE,
         xps.scheme = NULL,
         add.data   = TRUE,
         verbose    = TRUE)

    xpsMAS4(object, ...)

### Arguments

`xps.data` | object of class `DataTreeSet`.
`filename` | file name of ROOT data file.
`filedir` | system directory where ROOT data file should be stored.
`tmpdir` | optional temporary directory where temporary ROOT files should be stored.
`normalize` | logical. If `TRUE` scale normalization is used after an `ExprTreeSet` is obtained.
`sc` | value at which all arrays will be scaled to.
`option` | option determining the grouping of probes for summarization, one of ‘transcript’, ‘exon’, ‘probeset’; exon arrays only.
`exonlevel` | exon annotation level determining which probes should be used for summarization; exon/genome arrays only.
`update` | logical. If `TRUE` the existing ROOT data file `filename` will be updated.
`xps.scheme` | optional alternative `SchemeTreeSet`.
`add.data` | logical. If `TRUE` expression data will be included as slot `data`.
`verbose` | logical, if `TRUE` print status information.
`object` | object of class `DataTreeSet`.
`...` | arguments `filename`,`filedir`,`tmpdir`,`option`,`exonlevel`,`xps.scheme`.

### Details

This function computes the Affymetrix MAS 4.0 expression measure, i.e. the ‘Average Difference’ expression level, as implemented in XPS.

If `normalize=TRUE` then the expression levels will be scaled to `sc`. For `sc=0` the expression levels will be scaled to the mean expression level.

`xpsMAS4` is the `DataTreeSet` method called by function `mas4`, however, expression levels will not be scaled to a common mean expression level.

For further details see `mas5`.

### Value

An `ExprTreeSet`

### Note

In contrast to function `mas4`, expression levels computed with `xpsMAS4` will not be scaled to a common mean expression level.

### Author(s)

Christian Stratowa

### References

Affymetrix (1999) GeneChip Expression Analysis Algorithm Tutorial, Affymetrix Inc., Santa Clara, CA.

### See Also

`xpsMAS4`, `express`

### Examples

    ## first, load ROOT scheme file and ROOT data file
    scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
    data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

    data.mas4 <- mas4(data.test3,"tmp_Test3MAS4",tmpdir="",normalize=TRUE,sc=500, update=TRUE,verbose=FALSE)

    ## get data.frame
    expr.mas4 <- validData(data.mas4)
    head(expr.mas4)

    ## plot results (negative expression values!)
    if (interactive()) {
    boxplot(expr.mas4)
    }

    rm(scheme.test3, data.test3)
    gc()

[Package xps version 1.4.10 Index]