setQCEnvironment: Establish the appropriate QC environment for the specified...

In simpleaffy: Very simple high level analysis of Affymetrix data

Description

Affymetrix define a series of QC parameters for their arrays. Many of these rely on specific probeset that differ between arrays and are used to calculate things like 3'/5' ratios. See qc.affy for more details. These functions are used to set up the appropriate QC environment for the specified array. This is done by loading a configuration file, either from the packages data directory, or from the specified path. See the package vignette for details of the config file's syntax.

Usage

 setQCEnvironment(array,path=NULL)

Arguments

array	This should be the 'clean' cdf name of the array as generated by cleancdfname in the affy package.
path	Path to the file. By default, checks the package's own data directory - only needed if a defininition file is being specified manually, as described in the vignette.

Details

The usual way to get the 'clean' cdfname is as follows: cleancdfname(cdfName(eset)), where eset is an AffyBatch object.

Value

none.

Author(s)

Crispin J Miller

References

http://bioinformatics.picr.man.ac.uk/

See Also

qc

Examples

  setQCEnvironment("hgu133plus2cdf")
  setQCEnvironment(cleancdfname("HG-U133_Plus_2"))

simpleaffy documentation built on Nov. 8, 2020, 11:09 p.m.