simpleaffy (version 2.48.0)

qc: Generate QC stats from an AffyBatch object

Description

Generate QC metrix for Affymetrix data.

Usage

qc(unnormalised, ...)

Arguments

unnormalised

An AffyBatch object with nowt done to it

...

Any other parameters

Details

Affymetrix recommend a series of QC metrics that should be used to check that arrays have hybridised correctly and that sample quality is acceptable. These are discussed in the document 'QC and Affymetrix data' accompanying this package, and on the web at http://bioinformatics.picr.man.ac.uk. They are described in detail in the 'Expression Analysis Fundamentals' manual available from Affymetrix.

Before using this function you are strongly encouraged to read the 'QC and Affymetrix data' document, which contains detailed examples.

This function takes an AffyBatch object and generates a QCStats object containing a set of QC metrics. See qc.affy for more details.

See Also

qc.affy setQCEnvironment

Examples

  ## Not run: 
#     qcs <- qc(eset,eset.mas)
#   ## End(Not run)
  data(qcs)
  ratios(qcs)
  avbg(qcs)
  maxbg(qcs)
  minbg(qcs)
  spikeInProbes(qcs)
  qcProbes(qcs)
  percent.present(qcs)
  plot(qcs)
  sfs(qcs)
  target(qcs)
  ratios(qcs)