R: Generate Affymetrix Style QC Statistics

qc.affy {simpleaffy}

R Documentation

Generate Affymetrix Style QC Statistics

Description

Generate QC data for Affymetrix arrays

Usage

qc.affy(unnormalised,normalised=NULL,tau=0.015,logged=TRUE,
	cdfn=cdfName(unnormalised))

Arguments

`unnormalised`	An unnormalised raw `AffyBatch` object to call qc stats on
`normalised`	The same one, processed using `justMAS` (contains scale factors etc.). If not supplied, then the object gets calculated internally.
`tau`	used by detection p value
`logged`	True if the data is logged
`cdfn`	The cdf name for the array - can be used to specify a different set of probes to the default

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.

This function takes an (unnormalised) AffyBatch object, and (optionally) an ExprSet, with MAS expression calls produced by call.exprs and generates QC metrics. If the MAS calls are not supplied these are claculated internally.

Value

A QCStats object describing the supplied AffyBatch

Author(s)

Crispin J Miller

Examples

  ## Not run: 
     qcs <- qc(eset)
  
## 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)

[Package simpleaffy version 2.54.0 Index]