QCStats-class {simpleaffy}R Documentation

Class "QCStats"

Description

Holds Quality Control data for a set of Affymetrix arrays

Objects from the Class

Objects can be created by calls of the form qc(AffyBatch).

Slots

scale.factors:
Object of class "numeric" Scale factors used to scale the chips to the specified target intensity
target:
Object of class "numeric" The target intensity to which the chips were scaled
percent.present:
Object of class "numeric" Number of genes called present
average.background:
Object of class "numeric" The average background for the arrays
minimum.background:
Object of class "numeric" The minimum background for the arrays
maximum.background:
Object of class "numeric" The maximum background for the arrays
spikes:
Object of class "list" spiked in probes (e.g. biob, bioc...)
qc.probes:
Object of class "list" qc probes (e.g. gapdh 3,5,M,...)
arrayType:
The cdfName of the AffyBatch object used to create the object

Methods

avbg
signature(object = "QCStats"): average background
maxbg
signature(object = "QCStats"): maximum background
minbg
signature(object = "QCStats"): minimum background
spikeInProbes
signature(object = "QCStats"): the spike-in QC probes
qcProbes
signature(object = "QCStats"): the gapdh and actin QC probes
percent.present
signature(object = "QCStats"): no probesets called present
plot
signature(x = "QCStats"): Plot a QCStats object
sfs
signature(object = "QCStats"): scale factors
target
signature(object = "QCStats"): target scaling
ratios
signature(object = "QCStats"): 5'3' and 5'M ratios for QC Probes
arrayType
signature(object = "QCStats"): The type of array for which this QC stats object was generated

Author(s)

Crispin J Miller

See Also

qc


[Package simpleaffy version 2.18.0 Index]