yaqc.affy {yaqcaffy} | R Documentation |
Generate YAQC metrics for Affymetrix data.
yaqc.affy(object,tgt=100,tau=0.015,logged=FALSE)
object |
a object of type AffyBatch or ExpressionSet |
tgt |
the target intensity to which the chips should be scaled (used to calculated the GCOS intensities) |
tau |
used by detection p value |
logged |
to be used with an ExpressionSet object, defining if the
expression intensities are logged |
Affymetrix recommend a set of quality control metrics to check the quality of GeneChips expression arrays. This function applies the guidelines described in the Affymetrix Microarray Quality Control Consortium (MAQC) protocols to asses the succes of the hybridization. See the package vignette for more details.
This function takes a raw (unnormalised) AffyBatch
object or
and ExpressionSet
object. In the first case, it computess GCOS intensity
values, MAS expression calls(see call.exprs
) and other quality-related
metrics to generate an YAQCStats. If an ExpressionSet
object is provided,
only the $β$-actin, GAPDH and internal control values are computed.
An YAQCStats object describing the input object
Laurent Gatto
## loading data library(affydata) data(Dilution) ## qc analysis qobj <- yaqc(Dilution) show(qobj)