extractExpressionSet.ChipEffectSet: Extracts an in-memory ExpressionSet object

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

Extracts an in-memory ExpressionSet object

Description

Extracts an in-memory ExpressionSet object from a ChipEffectSet object. Note that any modifications done to the extracted object will not be reflected in the original chip-effect set.

Usage

## S3 method for class 'ChipEffectSet'
extractExpressionSet(this, ..., logBase=2, orderUnitsBy=c("asis", "lexicographic"),
  annotationPkg=NULL, verbose=FALSE)

Arguments

...	Optional argument passed to *extractMatrix().
logBase	An integer specifying the base to use when log-transforming the signals. If NULL, the signals are not transformed, but kept as is.
annotationPkg	(optional) A character string specifies a Bioconductor (ChipDb, CDF environment or PDInfo) annotation package, which then sets the 'annotation' slot of the returned object. If "ChipDb", "cdf" or "PDInfo" th corresponding ChipDB, CDF environment or PDInfo package is inferred from the CDF's chip type.
verbose	See Verbose.

Value

Returns an ExpressionSet-class object.

Author(s)

Henrik Bengtsson

See Also

For more information see ChipEffectSet.

HenrikBengtsson/aroma.affymetrix documentation built on Feb. 20, 2024, 9:07 p.m.