qc.affy {simpleaffy} | R Documentation |
Generates Affymetrix style QC statistics as defined in Affymetrix' 'Data Analysis Fundamentals' handbook
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))))
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 |
A QCStats object describing the supplied AffyBatch
Crispin J Miller
## Not run: qc <- qc(eset,eset.mas) ## End(Not run)