yaqcaffy (version 1.32.0)

YAQCStats-class: Class "YAQCStats"

Description

Holds Quality Control Data for a set of Affymetrix Arrays

Objects from the Class

Objects can be created by calls of the form yaqc providing AffyBatch or ExpressionSet instances as arguments. YAQCStats is a subclass of QCStats and uses the scale.factor, average.background, percent.present, arraytype and target attributes of it's super-class.

Slots

Class-specific slots:

log:

Object of class "logical" that specifies if expression values are in log2 form.

average.noise:

Object of class "numeric". The average noise for the arrays.

morespikes:

Object of class "matrix". More spiked in probes (e.g. r2biob5, r2biob3,...).

gcos.probes:

Object of class "matrix". GAPDH and $\beta$-actin qc probes (e.g. gapdh 3,5,M,...) containing the GCOS values.

bio.calls:

Object of class "matrix". BioB 5',3',M and BioC, BioC 5',3' present/absent/marginal calls .

objectVersion

Character describing the version of the library used to generate the YAQCStats object.

yaqcControlProbes

Object of class YaqcControlProbes that defines the different probes used for the quality control.

See also QCStats for slots inherited from super-class.

Methods

Methods inherited from the super-class:

target

signature(object = "YAQCStats"): Returns a numeric target value for MAS 5.0 normalization.

avbg

signature(object = "YAQCStats"): Returns a vector of the average background levels for each array.

minbg

signature(object = "YAQCStats"): Returns a vector of the minimum background levels for each array.

percent.present

signature(object = "YAQCStats"): Returns a vector listing the percentage of probesets called present on each array.

sfs

signature(object = "YAQCStats"): Returns a vector of scale factors for each array (as produced by the MAS 5.0 algorithm).

Class-specific methods:

isLog

signature(object = "YAQCStats"): Returns a logical specifying if the expression intensities are in log2 from.

moreSpikeInProbes

signature(object = "YAQCStats"): Returns a matrix of intensities for the internal spike probes.

gcosProbes

signature(object = "YAQCStats"): Returns a matrix of intensities for GAPDH and $\beta$-actin probes.

avns

signature(object = "YAQCStats"): Returns a vector listing the average noise levels for each array.

bioCalls

signature(object = "YAQCStats"): Returns a matrix of Present(P)/Marginal(M)/Absent(A) calls for the spike probes.

arrays

signature(object = "YAQCStats"): Returns the names of the arrays in the YAQCStats instance.

plot

signature(object = "YAQCStats"): visual representation of the qc metrics. (see yaqc.plot for more details).

summary

signature(x = "YAQCStats", latex = "logical"): The outliers of the YAQCStats quality control metrics are summerized and returned as a data frame. If latex is set to TRUE (default), the data frame is returned as a latex table (requires the xtable package).

show

signature(object = "YAQCStats"): displays the content of the object as a data frame.

merge

signature(x = "YAQCStats", y ="YAQCStats"): merges two compatible YAQCStats objects, i.e. that have the same values for the log, target and arraytype slots.

arrays

signature(object = "YAQCStats"): shows the array names of an YAQCStats objects.

objectVersion

signature(object = "YAQCStats"): Returns the version of the yaqcaffy package as a character used to create the given object.

getYaqcControlProbes

signature(object = "YAQCStats"): Returns the YaqcControlProbes object that has been used to generate the current YAQCStats object.

See Also

QCStats from package simpleaffy and YaqcControlProbes.