YAQCStats-class {yaqcaffy} | R Documentation |
Holds Quality Control data for a set of Affymetrix arrays
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.
log
:"logical"
that specifies if expression values are in log2 formaverage.noise
:"numeric"
The average noise for the arrays morespikes
:"matrix"
More spiked in probes (e.g. r2biob5, r2biob3,...) gcos.probes
:"matrix"
GAPDH and β-actin qc probes
(e.g. gapdh 3,5,M,...) containing the GCOS valuesbio.calls
:"matrix"
BioB 5',3',M and BioC, BioC 5',3'
present/absent/marginal calls signature(object = "YAQCStats")
: are intensities in log2 formsignature(object = "YAQCStats")
: average noisesignature(object = "YAQCStats")
: more spike-in probes signature(object = "YAQCStats")
: GCOS values of gapdh and actin QC probes signature(object = "YAQCStats")
: P/M/A calls for BioB, BioC and BioD spikes signature(object = "YAQCStats")
: shows the array names composing the YAQCStats
object signature(object = "YAQCStats")
: visual representation of the qc metrics signature(object = "YAQCStats")
: displays the content of the object as a data frame signature(object = "YAQCStats")
: merges two compatible YAQCStats objects, i.e. that have the same values for the log
, target
and arraytype
slots. signature(object = "YAQCStats")
: show the array names of an YAQCStats objects. Laurent Gatto
QCStats-class