R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 12 found.
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YAQCStats-class (Package: yaqcaffy) : Class "YAQCStats"

Holds Quality Control Data for a set of Affymetrix Arrays

● Data Source: BioConductor
● Keywords: classes
● Alias: YAQCStats-class, class:YAQCStats
● 0 images

YaqcControlProbes-class (Package: yaqcaffy) : Class "YaqcControlProbes"

The YAQCStats class stores the probes used for the quality control as a special class, namely the YaqcControlProbes class. This class encapsulated the probe names that are used the generate an YAQCStats object. Objects of this class are created with the probeSelectionInterface function. The hybridization, labelling and degradation probes are encapsulated in YaqcBioProbes, YaqcSpkProbes and YaqcDegProbes objects respectively. These can be retrieved with their respective accessors, as described below. Furthermore, an info function allows to retrieve or set a free text slot to describe the YaqcControlProbes object.

● Data Source: BioConductor
● Keywords: classes
● Alias: YaqcBioProbes-class, YaqcControlProbes-class, YaqcDegProbes-class, YaqcSpkProbes-class, bio, bio,YaqcBioProbes-method, bio,YaqcControlProbes-method, bio-methods, class:YaqcBioProbes, class:YaqcControlProbes, class:YaqcDegProbes, class:YaqcSpkProbes, deg, deg,YaqcControlProbes-method, deg,YaqcDegProbes-method, deg-methods, info, info,YaqcControlProbes-method, info<-, info<-,YaqcControlProbes-method, show,YaqcBioProbes-method, show,YaqcControlProbes-method, show,YaqcDegProbes-method, show,YaqcSpkProbes-method, spk, spk,YaqcControlProbes-method, spk,YaqcSpkProbes-method, spk-methods
● 0 images

getAllInt (Package: yaqcaffy) : Get the summerized MAS5 values for a given spike probe

This function retrieves the expression intensities prvided by the object of class "YAQCStats" for the probe which names are compatible with the given pattern and return their mean value.

● Data Source: BioConductor
● Keywords: misc
● Alias: getAllInt
● 0 images

getBioProbes (Package: yaqcaffy) : Get the names of the Bio spike probes on the array

This function returns all the AFFX-Bio probes names that are located on the given GeneChip.

● Data Source: BioConductor
● Keywords: misc
● Alias: getBioProbes
● 0 images

getOutliers (Package: yaqcaffy) : Get outliers for the different YAQCStatsObject slots

This function retrives the outliers fot the different quality control metrics stored in a YAQCStatsObject. Outliers are defined as being outside of the mean +/- 2 stdev range or mean/2, mean*1.5 for the scale factor.

● Data Source: BioConductor
● Keywords: misc
● Alias: getOutliers
● 0 images

getQCRatios (Package: yaqcaffy) : Compute qc probe ratios using GCOS intensity values

This function computes the 3'/5' ratios of the GAPDh and β-actin qc probes using the GCOS intensity values.

● Data Source: BioConductor
● Keywords: misc
● Alias: getQCRatios
● 0 images

getRatioProbes (Package: yaqcaffy) : Get the names of degradation control probes on the array

This function returns the probes names used for degradation control that are located on the given GeneChip.

● Data Source: BioConductor
● Keywords: misc
● Alias: getRatioProbes
● 0 images

getSpikeProbes (Package: yaqcaffy) : Get the names of all spike probes on the array

This function returns all the spike probes (i.e. BioB-3', BioD-5', Lys-3, ...) that are located on the given GeneChip.

● Data Source: BioConductor
● Keywords: misc
● Alias: getSpikeProbes
● 0 images

probeSelectionInterface (Package: yaqcaffy) : Tcltk Interface to Generate an Instance of YaqcControlProbes for a given Chip Set

probeSelectionInterface starts a tcltk graphical user interface (GUI) that allows the user to choose the probes to be used for subsequent quality analyses with the yaqcaffy package. The probes are selected on basis of the features of a given set of Affymetrix Genechips provided as input. The list of probes can be pre-filtered to display only control probes (i.e starting by AFFX) or all probes on the Genechip can be shown.

● Data Source: BioConductor
● Keywords: misc
● Alias: probeSelectionInterface
● 0 images

reprodPlot (Package: yaqcaffy) : Plot human whole genome GeneChips reproductibility

Compares Affymetrix Human Genome U133 Plus 2.0 Arrays to a subset of the MAQC arrays for a RNA reference.

● Data Source: BioConductor
● Keywords: misc
● Alias: reprodPlot
● 0 images