qc.affy: Generate Affymetrix Style QC Statistics

In simpleaffy: Very simple high level analysis of Affymetrix data

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)

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