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
bioB:
Object of class "character" bioB present call
bioC:
Object of class "character" bioC present call
bioD:
Object of class "character" bioD present call
creX:
Object of class "character" creX present call
gapdh3:
Object of class "numeric" gapdh 3' intensity
gapdhM:
Object of class "numeric" gapdh M intensity
gapdh5:
Object of class "numeric" gapdh 5' intensity
actin3:
Object of class "numeric" beta actin 3' intensity
actinM:
Object of class "numeric" beta actin M intensity
actin5:
Object of class "numeric" beta actin 5' intensity

Methods

actin35
signature(object = "QCStats"): beta actin 3' 5' ratio
actin3
signature(object = "QCStats"): beta actin 3' intensity
actin3M
signature(object = "QCStats"): beta actin 3' M ratio
actin5
signature(object = "QCStats"): beta actin 5' intensity
actinM
signature(object = "QCStats"): beta actin M intensity
avbg
signature(object = "QCStats"): average background
bioB
signature(object = "QCStats"): bioB call
bioC
signature(object = "QCStats"): bioC call
bioD
signature(object = "QCStats"): bioD call
creX
signature(object = "QCStats"): creX call
gapdh35
signature(object = "QCStats"): gapdh 3' 5' ratio
gapdh3
signature(object = "QCStats"): gapdh 3' intensity
gapdh3M
signature(object = "QCStats"): gapdh 3' M ratio
gapdh5
signature(object = "QCStats"): gapdh 5' inensity
gapdhM
signature(object = "QCStats"): gapdh M intensity
maxbg
signature(object = "QCStats"): maximum background
minbg
signature(object = "QCStats"): minimum background
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

Author(s)

Crispin J Miller

See Also


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