Bscore
(Package: cellHTS) :
B score normalization
Correction of plate and spatial effects of the data xraw of a cellHTS object using the B score method. Using this method, a two-way median polish is fitted in a per-plate basis to account for row and column effects. Optionally, the obtained residuals within each plate can be further divided by their median absolute deviations to standardize for plate-to-plate variability. Optionally, a transformation to z-scores can be performed.
● Data Source:
BioConductor
● Keywords: manip
● Alias: Bscore
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ROC
(Package: cellHTS) :
Creates an object of class "ROC" which can be plotted as a ROC curve
The function ROC construct an object of S3 class ROC, which represents a receiver-operator-characteristic curve, from the data of the annotated positive and negative controls in a scored cellHTS object.
● Data Source:
BioConductor
● Keywords: univar
● Alias: ROC, lines.ROC, plot.ROC
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annotate
(Package: cellHTS) :
Annotates the gene IDs of a given cellHTS object
Annotate the gene IDs of a given cellHTS object.
● Data Source:
BioConductor
● Keywords: manip
● Alias: annotate, annotate.cellHTS
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configure
(Package: cellHTS) :
Configures the plates and plate result files
Annotate the plates and the plate result files of a given cellHTS object.
● Data Source:
BioConductor
● Keywords: manip
● Alias: configure, configure.cellHTS
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getEnVisionRawData
(Package: cellHTS) :
Read a plate file obtain from EnVision Plate Reader
Import functions to read a plate file obtained from EnVision Plate Reader. These functions should be set as the import function of readPlateData through the argument importFun when reading plate result files obtained from EnVision plate reader.
● Data Source:
BioConductor
● Keywords: manip
● Alias: getEnVisionCrosstalkCorrectedData, getEnVisionRawData
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getLibraryPlate
(Package: cellHTS) :
384-well plate assay format to a 96-well plate library format
Given a cellHTS object with data from an assay conducted in 384-well plate format, resulting from the combination of four consecutive 96-well plates of a reagent library, this function gives the plate identifiers for the 96-well plates.
● Data Source:
BioConductor
● Keywords: manip
● Alias: getLibraryPlate
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getMatrix
(Package: cellHTS) :
Create a matrix with replicate data in columns
Given an array of raw or normalized intensities (xraw or xnorm) of a cellHTS object, creates a matrix with the data from the chosen channel.
● Data Source:
BioConductor
● Keywords: manip
● Alias: getMatrix
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imageScreen
(Package: cellHTS) :
Experiment-wide quality control plot of a cellHTS object
Experiment-wide quality control plot of a scored cellHTS object.
● Data Source:
BioConductor
● Keywords: manip
● Alias: imageScreen
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1 images
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normalizeChannels
(Package: cellHTS) :
Normalization of dual-channel data and data transformation
Normalizes and/or transforms dual-channel data xraw of a given cellHTS object by applying the function defined in fun. The default is to take the ratio between the second and first channels (r2/r1). Correction of plate-to-plate variations may also be performed.
● Data Source:
BioConductor
● Keywords: manip
● Alias: normalizeChannels
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normalizePlates
(Package: cellHTS) :
Plate-wise data normalization, and data transformation
Normalization of the data xraw in a cellHTS object. This is done separately for each plate, replicate and channel. Optionally, a data transformation such as log, and a transformation to z-scores can be performed.
● Data Source:
BioConductor
● Keywords: manip
● Alias: normalizePlates, plate effects
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