oligoOld: Preprocessing tools for oligonucleotide arrays

Description Usage Arguments Details Examples

Accessors and replacement methods for the PM/MM/BG matrices.

intensity(object)
mm(object, subset = NULL, target='core')
pm(object, subset = NULL, target='core')
bg(object, subset = NULL)
mm(object, subset = NULL, target='core')<-value
pm(object, subset = NULL, target='core')<-value
bg(object)<-value

`object`	`FeatureSet` object.
`subset`	Not implemented yet.
`value`	`matrix` object.
`target`	One of 'probeset', 'core', 'full', 'extended'. This is ignored if the array design is something other than Gene ST or Exon ST.

For all objects but TilingFeatureSet, these methods will return matrices. In case of TilingFeatureSet objects, the value is a 3-dimensional array (probes x samples x channels).

intensity will return the whole intensity matrix associated to the object. pm, mm, bg will return the respective PM/MM/BG matrix.

When applied to ExonFeatureSet or GeneFeatureSet objects, pm will return the PM matrix at the transcript level ('core' probes) by default. The user should set the target argument accordingly if something else is desired. The valid values are: 'probeset' (Exon and Gene arrays), 'core' (Exon and Gene arrays), 'full' (Exon arrays) and 'extended' (Exon arrays).

The target argument has no effects when used on designs other than Gene and Exon ST.

if (require(maqcExpression4plex) & require(pd.hg18.60mer.expr)){
xysPath <- system.file("extdata", package="maqcExpression4plex")
xysFiles <- list.xysfiles(xysPath, full.name=TRUE)
ngsExpressionFeatureSet <- read.xysfiles(xysFiles)
pm(ngsExpressionFeatureSet)[1:10,]
}