simpleaffy (version 2.48.0)

simpleaffy-deprecated: Does simpleaffy have a QC definition file for the specified array?

Description

The underlying implementation of simpleaffy has changed significantly and it now represents QC parameters differently. In particular, it loads only the QC data for the specified array type. A call to any of these functions loads the appropriate environment specifed by name. They therefore been deprecated and WILL disappear from simpleaffy in the future.

Usage

getTao(name)
  getAlpha1(name)
  getAlpha2(name)
  getActin3(name)
  getActinM(name)
  getActin5(name)
  getGapdh3(name)
  getGapdhM(name)
  getGapdh5(name)
  getAllQCProbes(name)
  getBioB(name)
  getBioC(name)
  getBioD(name)
  getCreX(name)
  getAllSpikeProbes(name)
  haveQCParams(name)

Arguments

name

The 'clean' CDF name of the array (i.e. the result of calling cleancdfname on the cdfName of the AffyBatch object containing the array data of interest.

Value

• None.

Details

Each of these functions has been replaced by a new function of the form qc.get.. In order to support ratios other than gapdh and beta-actin, the appropriate way to get ratios is now to use qc.get.ratios, which will return a table containing all suggested ratio calculations for the array. Similarly, qc.get.spikes will return a table containing all spike probesets for the array.

References

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

See Also

setQCEnvironment qc qc.ok cdfName cleancdfname qc.get.ratios qc.get.spikes qc.get.probes

Examples

#old
  getBioB("hgu133plus2cdf")
  getActin3("hgu133plus2cdf")
  getActinM("hgu133plus2cdf")
  getActin5("hgu133plus2cdf")
  #new
  setQCEnvironment("hgu133plus2cdf")
  qc.get.spikes()["bioB"]
  r <- qc.get.probes()
  r["actin3"]
  r["actinM"]
  r["actin5"]