YAQCStats-class {yaqcaffy}R Documentation

Class "YAQCStats"

Description

Holds Quality Control data for a set of Affymetrix arrays

Objects from the Class

Objects can be created by calls of the form yaqc(object) where object is of class AffyBatch of ExpressionSet. YAQCStats is a subclass of QCStats and uses the scale.factor, average.background and percent.present, arraytype and target attributes of it's subclass.

Slots

log:
Object of class "logical" that specifies if expression values are in log2 form
average.noise:
Object of class "numeric" The average noise for the arrays
morespikes:
Object of class "matrix" More spiked in probes (e.g. r2biob5, r2biob3,...)
gcos.probes:
Object of class "matrix" GAPDH and β-actin qc probes (e.g. gapdh 3,5,M,...) containing the GCOS values
bio.calls:
Object of class "matrix" BioB 5',3',M and BioC, BioC 5',3' present/absent/marginal calls

Methods

isLog
signature(object = "YAQCStats"): are intensities in log2 form
avns
signature(object = "YAQCStats"): average noise
moreSpikeInProbes
signature(object = "YAQCStats"): more spike-in probes
gcosProbes
signature(object = "YAQCStats"): GCOS values of gapdh and actin QC probes
bioCalls
signature(object = "YAQCStats"): P/M/A calls for BioB, BioC and BioD spikes
arrays
signature(object = "YAQCStats"): shows the array names composing the YAQCStats object
plot
signature(object = "YAQCStats"): visual representation of the qc metrics
show
signature(object = "YAQCStats"): displays the content of the object as a data frame
merge
signature(object = "YAQCStats"): merges two compatible YAQCStats objects, i.e. that have the same values for the log, target and arraytype slots.
arrays
signature(object = "YAQCStats"): show the array names of an YAQCStats objects.

Author(s)

Laurent Gatto

See Also

QCStats-class


[Package yaqcaffy version 1.2.0 Index]