readIntensities {arrayMagic}R Documentation

readIntensities

Description

The function takes the data.frame slideDescription as input and reads the listed image analysis raw data files of the column slideNameColumn; cf. function readpDataSlides. Each image analysis raw data file must contain tab separated columns and a header line - not necessarily at the top of the file; cf. the arguments removePatterns and skip. Each file may only contain the information for one channel, cf. argument channelColumn. The raw data information is returned as an object of class arrayData. Note: All image analysis quantification (=raw data) files have to correspond to the same type of microarray.

Usage

readIntensities(slideDescription, fileNameColumn="fileName", slideNameColumn, channelColumn = NULL, loadPath=".", type = "GenePix", spotAnnoColumns = NULL, dataColumns = NULL, removePatterns = NULL, skip = NULL, spotIdentifier, ..., verbose = TRUE)

Arguments

slideDescription data.frame; required; default: missing. (cf. the return value of the function readpDataSlides) The data.frame must contain at least one column; this column has to be named as the argument fileNameColumn. It may additionally contain a column named slideNameColumn.
fileNameColumn character string; required; default: "fileName". fileNameColumn specifies the column which contains all image quantification result files in the data.frame of argument slideDescription.
slideNameColumn character string; optional; default missing; refers to the data.frame of argument slideDescription. If slideNameColumn is missing the value is set to fileNameColumn.
channelColumn named vector of character strings; optional; default NULL. If the data.frame of argument slideDescription contains information for each channel of every slide/hybridisation separately, the channelColumn vector contains the column name of the data.frame of argument slideDescription used to specify the channel. If length(channelColumn) == 1 the character strings "green" and "red" are assumed to be used for the coding, otherwise names(channelColumn) must contain: c("channelColumnName","green","red").
loadPath character string; required; default: ".". The path is used to load the image quantification result files; note: "." refers to the working directory.
spotIdentifier character string; optional; default missing. spotIdentifier specifies the column in the image analysis result files which contain spot or gene identifiers.
type character string; required; possible values: "GenePix", "ScanAlyze", "generic" and "genericOneFilePerChannel"; cf. Details section. Note: value "generic" requires the arguments spotAnnoColumns, dataColumns and possibly skip and removePatterns, value "genericOneFilePerChannel" additionally requires the argument "channelColumn"; whereas "GenPix" and "ScanAlyze" use predefined values if not otherwise specified; default: "GenePix".
spotAnnoColumns vector of character strings; the column names of the image analysis data file. The columns must contain the same information for all files, e.g. the information on the layout of the microarray. The argument spotIdentifier is automatically added to the vector if not already included; default: NULL
dataColumns named vector of character strings; the column names of the image analysis data file. The columns contain the raw intensities values of each spot; names(dataColumns) must contain: c("greenForeground", "greenBackground", "redForeground", "redBackground"); default: NULL
removePatterns vector of character string(s) each defining a regular expression; default: NULL; all lines of each image analysis raw data file, which match any of the regular expression(s) are discarded.
skip integer; default: NULL; number of lines skipped in each image analysis data file; Argument skip applies after all lines matched by one of the arguments of removePatterns have been discarded.
... further arguments which are passed to read.table. A function which is used inside this function. The arguments must not include sep, header, as.is and skip (for skip cf. above).
verbose logical; required; default TRUE

Details

Details on the argument type: type="GenePix" defines spotAnnoColumns = c("Block", "Column", "Row", "Name", "ID") and dataColumns = c("F532.Median", "B532.Median", "F635.Median", "B635.Median") and corresponding names(dataColumns) = c("greenForeground", "greenBackground", "redForeground", "redBackground"), a dynamically determined argument skip = grep("Block...Column", imageFile) - 1 and removePatterns = NULL, whereas type="ScanAlyze" defines spotAnnoColumns = c( "HEADER", "SPOT", "GRID", "ROW", "COL" ) and dataColumns = c("CH1I", "CH1B", "CH2I", "CH2B") and corresponding names(dataColumns) = c("greenForeground", "greenBackground", "redForeground", "redBackground"), skip = 0 and removePatterns = c("^REMARK").

Value

object of class arrayData

Author(s)

Andreas Buness <a.buness@dkfz.de>

See Also

readpDataSlides, arrayData-class

Examples


   

 

[Package arrayMagic version 1.5.8 Index]