mas5 {xps} | R Documentation

## MAS 5.0 Expression Measure

### Description

This function converts a `DataTreeSet` into an `ExprTreeSet` using the XPS implementation of Affymetrix's MAS 5.0 expression measure.

### Usage

    mas5(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)

    xpsMAS5(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 5.0 expression measure as implemented in XPS. Although this implementation is based on the Affymetrix ‘sadd_whitepaper.pdf’, it can be used to compute an expression level for both expression arrays and exon arrays. For exon arrays it is necessary to supply the requested `option` and `exonlevel`.

Following `option`s are valid for exon arrays:

`transcript`: | expression levels are computed for transcript clusters, i.e. probe sets containing the same ‘transcript_cluster_id’.
`exon`: | expression levels are computed for exon clusters, i.e. probe sets containing the same ‘exon_id’, where each exon cluster consists of one or more `probeset`s.
`probeset`: | expression levels are computed for individual probe sets, i.e. for each ‘probeset_id’.

Following `exonlevel` annotations are valid for exon arrays:

| `core`: | probesets supported by RefSeq and full-length GenBank transcripts.
| `metacore`: | core meta-probesets.
| `extended`: | probesets with other cDNA support.
| `metaextended`: | extended meta-probesets.
| `full`: | probesets supported by gene predictions only.
| `metafull`: | full meta-probesets.
| `ambiguous`: | ambiguous probesets only.
| `affx`: | standard AFFX controls.
| `all`: | combination of above (including affx).

Following `exonlevel` annotations are valid for whole genome arrays:

| `core`: | probesets with category ‘unique’, ‘similar’ and ‘mixed’.
| `metacore`: | probesets with category ‘unique’ only.
| `affx`: | standard AFFX controls.
| `all`: | combination of above (including affx).

Exon levels can also be combined, with following combinations being most useful:

`exonlevel="metacore+affx"`: | core meta-probesets plus AFFX controls
`exonlevel="core+extended"`: | probesets with cDNA support
`exonlevel="core+extended+full"`: | supported plus predicted probesets

Exon level annotations are described in the Affymetrix whitepaper ‘exon_probeset_trans_clust_whitepaper.pdf’.

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.

If `update=TRUE` then the existing `ROOT` file `filename` will be updated, however, this is usually only recommended as option for function `express`.

In order to use an alternative `SchemeTreeSet` set the corresponding SchemeTreeSet `xps.scheme`.

`xpsMAS5` is the `DataTreeSet` method called by function `mas5`, however, expression levels will not be scaled to a common mean expression level.

### Value

An `ExprTreeSet`

### Note

In contrast to function `mas5`, expression levels computed with `xpsMAS5` will not be scaled to a common mean expression level.

### Author(s)

Christian Stratowa

### References

Affymetrix (2002) Statistical Algorithms Description Document, Affymetrix Inc., Santa Clara, CA, whitepaper. http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf

Affymetrix (2005) Exon Probeset Annotations and Transcript Cluster Groupings, Affymetrix Inc., Santa Clara, CA, exon_probeset_trans_clust_whitepaper.pdf.

### See Also

`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.mas5 <- mas5(data.test3,"tmp_Test3MAS5",tmpdir="",normalize=TRUE,sc=500,update=TRUE,verbose=FALSE)

    ## get data.frame
    expr.mas5 <- validData(data.mas5)
    head(expr.mas5)

    ## plot results
    if (interactive()) {
    boxplot(data.mas5)
    boxplot(log2(expr.mas5))
    }

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

[Package xps version 1.4.10 Index]