QCStats-class: Class "QCStats"

In simpleaffy: Very simple high level analysis of Affymetrix data

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

Author(s)

Crispin J Miller

See Also

qc

simpleaffy documentation built on Nov. 8, 2020, 11:09 p.m.