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.