QCStats-class: 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 bioBCalls:- Object of class
"character" The
detection PMA (present / marginal / absent) calls of bioB spike-in
probes 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