cellHTS (version 1.42.0)

cellHTS-class: A class for data from cell-based high-throughput assays performed in plate format.

Description

Container for data and experimental meta-data from cell-based high-throughput assays performed in plate format. Typical applications are RNA interference or small molecular compound screens. The class extends the NChannelSet class. Data are from experiments where the same set of reagents (probes) where used. The class can represent data from multi-channel assays.

The data can be thought of as being organised in a two- or three-dimensional array as follows:

• The first dimension corresponds to reagents (e.g. siRNAs, chemical compounds) that were used in the assays. For example, if the screen used 100 plates of 384 wells (24 columns, 16 rows), then the first dimension has size 38,400, and thecellHTSobject keeps track of plate ID, row, and column associated with each element. For historic reasons, and because we are using infrastructure that was developed for microarray experiments, the following terms are used synonymously for the elements of the first dimension: reagents, features, probes, genes.
• The second dimension corresponds to assays, including replicates and different experimental conditions (cell type, treatment, genetic background). A potentially confusing terminology is that the data structure that annotates the second dimension is calledphenoData. This is because we are using infrastructure (theNChannelSetclass) that uses this unfortunate term for this purpose. The software provides methodology for replicate summarization and scoring, however more complicated experimental designs are not directly supported. Multi-purpose tools likelmFitin thelimmapackage should be consulted.
• The (optional) third dimension corresponds to different channels (e.g. different luminescence reporters)

Objects from the Class

Objects can be created by calls of the form new("cellHTS", assayData, phenoData, ...). See the examples below.

Extends

Class NChannelSet, directly.

See Also

NChannelSet readPlateList annotate configure writeTab state Data normalizePlates ROC

Examples

showClass("cellHTS")
    showMethods(class="cellHTS")
  
    ## An empty cellHTS
    obj <- new("cellHTS")

    data("KcViabSmall")
    KcViabSmall
    state(KcViabSmall)
    ## Replicate 1 as a cellHTS object
    y <- KcViabSmall[,1] 
    compare2cellHTS(KcViabSmall, y)
    data("KcViab")
    compare2cellHTS(KcViab, KcViabSmall)