qc.affy {simpleaffy}R Documentation

Generate Affymetrix Style QC Statistics

Description

Generates Affymetrix style QC statistics as defined in Affymetrix' 'Data Analysis Fundamentals' handbook

Usage

qc.affy(unnormalised,normalised=NULL,logged=TRUE,
        tau=getTao(cleancdfname(cdfName(unnormalised))),
        alpha1=getAlpha1(cleancdfname(cdfName(unnormalised))),
        alpha2=getAlpha2(cleancdfname(cdfName(unnormalised))),
        bioB=getBioB(cleancdfname(cdfName(unnormalised))),
        bioC=getBioC(cleancdfname(cdfName(unnormalised))),
        bioD=getBioD(cleancdfname(cdfName(unnormalised))),
        creX=getCreX(cleancdfname(cdfName(unnormalised))),
        gapdh3=getGapdh3(cleancdfname(cdfName(unnormalised))),
        gapdhM=getGapdhM(cleancdfname(cdfName(unnormalised))),
        gapdh5=getGapdh5(cleancdfname(cdfName(unnormalised))),
        actin3=getActin3(cleancdfname(cdfName(unnormalised))),
        actinM=getActinM(cleancdfname(cdfName(unnormalised))),
        actin5=getActin5(cleancdfname(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.
logged True if the data is logged
tau Specify the tau value rather than the default for the arrays
alpha1 Specify the alpha1 value rather than the default for the arrays
alpha2 Specify the alpha2 value rather than the default for the arrays
bioB Specify the bioB value rather than the default for the arrays
bioC Specify the bioC value rather than the default for the arrays
bioD Specify the bioD value rather than the default for the arrays
creX Specify the crex value rather than the default for the arrays
gapdh3 Specify the gapdh3 value rather than the default for the arrays
gapdhM Specify the gapdhM value rather than the default for the arrays
gapdh5 Specify the gapdh5 value rather than the default for the arrays
actin3 Specify the actin3 value rather than the default for the arrays
actinM Specify the actinM value rather than the default for the arrays
actin5 Specify the actin5 value rather than the default for the arrays

Value

A QCStats object describing the supplied AffyBatch

Author(s)

Crispin J Miller

Examples

  ## Not run: 
     qc <- qc(eset,eset.mas)
  
## End(Not run)

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