Read a set of plate results obtained from a HTanalyser plate reader
Reads input files (specified by the argument
filenames) containing replicate data for the same set of assay plates and obtained using an HTanalyser.
The number of replicates corresponds to the number of given files (
length(filenames)), while the total number of plates should be given by the argument
vector of characters giving the name(s) of the input file(s) obtained in a HTanalyser plate reader and containing the set of measurements for each set of replicate plates (see details).
can be either a character vector with the same length as
a character of length 1 with the experiment name.
an integer value indicating the number of plates in the input file(s).
a logical value, if TRUE, the function reports some of its intermediate progress. Defaults to the state of
This function reads input files obtained in a HTanalyser plate reader for a multi-plate format screening experiment. Data for the same set of replicate measurements of all plates are expected to come in a single input file.
So, the argument
filenames should be a character vector specifying the name of the input files for each replicate.
Each of these files is expected to contain data for a total of
nrPlates assay plates. It contains meta-experimental data together with plate measurements in a matrix-like format. The same type of format is expected for each of the
nrPlates contained in each input file indicated in
The input files should be suitable to be used as input for
The following metadata fields are expected to be repeated along the input file(s) for each assay plate:
Microplate format, indicates the plate format used in the screen. Should be the same across plates.
Barcode, this field is used to uniquely identify each assay plate.
Method ID, indicates the method used to perform the assay. Should be the same for every plate.
Data, indicates the type of data and should be the same for every plate.
Units, indicates the units of the readings. Should be the same for every plate.
Display format, indicating the numeric format used to display the data measurements. Should be the same along plates.
This function expects that the next line after the meta field "Display format" for a given plate contains the column numbers (
1:ncol) which are then followed by the matrix of measurements in each well. Each entry of the data matrix corresponds to a position in the assay plate with coordinates
(row, col), except the first column, which gives the row ID, as upper letters (A, B, ...).
An object of class
cellHTS, which extends the
After calling this function, the content of the following slots is as follows:
an object of class
the information about the plate and well
identifiers for each plate measurement are stored in columns
a list, where each component contains a
copy of the measurement data of a given plate, replicate and
channel. Its length corresponds to the
number of rows of
a data.frame containing the columns "Filename",
"Plate", "Replicate", "Channel" and "status". Each row of this slot
makes the correspondence between a given component (name given in
column "Filename") in the list stored in slot
Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.
To read a collection of plate result files with measurements of a single
plate and replicate, see
1 2 3 4
datadir <- system.file("KcCellTiter", package = "cellHTS2") x <- readHTAnalystData(filenames = c("KcCellTiter0607.txt", "KcCellTiter0707.txt"), name="KcData", path=datadir, nrPlates=3L) x <- configure(x, confFile = "Plateconf.txt", logFile="Screenlog.txt", descripFile = "Description.txt", path = datadir)
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