calculateBaseline.ChipEffectSet: Estimates the baseline signal chromosome by chromosome

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

Estimates the baseline signal chromosome by chromosome

Description

Estimates the baseline signal chromosome by chromosome.

Usage

## S3 method for class 'ChipEffectSet'
calculateBaseline(this, chromosomes=NULL, ploidy=2, defaultPloidy=NA, all=FALSE,
  force=FALSE, verbose=FALSE, ...)

Arguments

chromosomes	An integer vector specifying for which chromsosomes the baseline should be estimated. If NULL, all chromosomes are considered.
ploidy	An integer specifying the ploidy that the baseline should have.
defaultPloidy	An integer specifying the default ploidy of chromosomes that have not explicitly been allocated one.
all	If TRUE, signals are averaged also for cells that are not on the genome.
force	If TRUE, the CEL file that stores the is recreated.
verbose	See Verbose.
...	Not used.

Author(s)

Henrik Bengtsson

See Also

getAverageFile(). For more information see ChipEffectSet.

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