cellHTS2 Package Overview
This package provides data structures and algorithms for
cell-based high-throughput assays performed in plate
format. Typical applications are RNA interference
or small molecular compound screens.
The most important data class is
which extends the
Full help on methods and associated functions is available from within class help pages.
Introductory information is available from vignettes, type
A full listing of documented topics is available in HTML view by
help.start() and selecting the
cellHTS2 package from the
Packages menu or via
Ligia P. Bras
Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.
Below, we present a list of ‘high level’ functions in the celHTS2 package together with a brief description of what they do.
readPlateList read a collection of plate reader data files.
readHTAnalystData read input files from a HTanalyser plate reader containing data for a set of plate replicates.
Screen configuration and annotation:
Data accesses and replaces the
assayData slot of a cellHTS object. It returns a 3D array with dimensions number of features (product between the number of wells per plates and the number of plates) x number of samples (or replicates) x number of channels.
intensityFiles returns a list, where each component contains a
copy of the imported input data files.
plate plate identifier for each feature (well).
plateConf returns a data.frame that contains what was read from the plate configuration input file (except the first two header rows) during the screen configuration step.
plateList returns a data.frame containing what was read from the plate list file,
plus a column
status of type character that contains
the string "OK" if the data import appeared to have gone well, and the respective error or warning
position gives the well number for each feature (well) within each plate.
screenLog returns a data.frame containing what was read from the screen log input file during the screen configuration step.
well gives the alphanumeric identifier (e.g. A01, A02, ...) for each well and plate.
normalizePlates per-plate data transformation, normalization and variance adjustment.
Bscore correction of plate and spatial effects using the B score method (without variance adjustment of the residuals).
spatialNormalization correction of spatial effects by fitting a polynomial surface within each plate using local regression (
robust local fit). Uses a second degree polynomial (local quadratic fit). Only wells containing "sample" are considered to fit the models.
scoreReplicates transform per-replicate values into scores.
summarizeReplicates summarizes between normalized and
scored replicate values, obtaining a single value for each probe.
convertWellCoordinates converts between different ways of specifying well coordinates within a plate.
For example, wells can be identified by an alphanumeric character (e.g. "B02" or c("B", "02")) or by an integer value (e.g. 26).
getZfactor calculates per-experiment Z'-factor of data stored in a
The Z'-factor is a measure that quantifies the separation between the distribution of positive and negative controls.
plotSpatialEffects this function plots the per-plate row and column effects estimated by the B score method or by the spatial normalization.
oneRowPerId rearranges dataframe entries such that there is exactly one row
writeTab this function is a wrapper for the function
write.table to write the contents of
assayData slot of a
cellHTS object to a tab-delimited file. If the object is already annotated, the probe information (
fData(object)@GeneID) is also added.