Read a set of plate results obtained from a HTanalyser plate reader

Description

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 nrPlates.

Usage

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readHTAnalystData(filenames, path=dirname(filenames), name, nrPlates, verbose=interactive())

Arguments

filenames

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).

path

can be either a character vector with the same length as filenames or a character of length 1 indicating the path in which to find the input file(s) filenames. By default, it can extract the path from filenames.

name

a character of length 1 with the experiment name.

nrPlates

an integer value indicating the number of plates in the input file(s).

verbose

a logical value, if TRUE, the function reports some of its intermediate progress. Defaults to the state of interactive().

Details

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 filenames. The input files should be suitable to be used as input for readLines.

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, ...).

Value

An object of class cellHTS, which extends the class NChannelSet. After calling this function, the content of the following slots is as follows:

assayData

an object of class AssayData containing the imported measurement data. Each matrix represents a single channel, and each sample (replicate) corresponds to a column. Thus, the total number of rows in each matrix corresponds to the product between the number of wells per plate and the number of assay plates.

phenoData

the argument name is stored in its column assay.

featureData

the information about the plate and well identifiers for each plate measurement are stored in columns plate and well of this slot.

intensityFiles

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 plateList.

plateList

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 intensityFiles (i.e. plate) and its respective plate, replicate and channel number. Thus, this data.frame contains as many rows as the product between the total number of plates, replicates and channels. The last column named status is of type character and contains the string "OK" indicated the success status of the data import.

Author(s)

W. Huber huber@ebi.ac.uk, Ligia Bras ligia@ebi.ac.uk

References

Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.

See Also

To read a collection of plate result files with measurements of a single plate and replicate, see readPlateList.

Examples

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    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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