ExiMiR function for reading Exiqon raw data into an AffyBatch object.

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Description

This function reads Exiqon raw data in ImaGene file format and creates an AffyBatch object.

Usage

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ReadExi(txtfile.path=getwd(),
        galname=NULL,
        description=NULL,
	notes='',
	rm.background=FALSE,
	verbose=TRUE)

Arguments

txtfile.path

Character vector. It contains the path to the folder containing the samplesinfo.txt file and the Exiqon raw data files in ImaGene txt format.

galname

Character vector. The default value is NULL. In this case the GAL annotation environment used by ReadExi for generating the resulting AffyBatch object is lost. Assigning galname a non-empty value allows to control this GAL environment, which is useful in two specific situations. First, it gives a handle to this GAL annotation environment for later use. Second, if an adequate GAL annotation environment already exists in the memory (e.g. after having been generated by ReadExi or by make.gal.env), galname allows to force ReadExi to use it for generating the resulting AffyBatch object.

description

Object of class MIAME, as specified in the documentation of the AffyBatch object provided in the affy package.

notes

Character vector, as specified in the documentation of the AffyBatch object provided in the affy package.

rm.background

Logical. This option is kept for compatibility reasons but it is not used anymore. See the NormiR options for background correction.

verbose

Logical. The default value is TRUE. The details of the function execution are displayed on the console.

Details

The Exiqon miRNA raw expression data are normally in ImageGene txt file format and accompanied by a samplesinfo.txt description file. It enumerates the names of the sample files for each channel. Therefore the txtfile.path argument of ReadExi must be a folder that contains the ImageGene and the samplesinfo.txt files. If this is not the case, ReadExi stops.

The galname argument of ReadExi must be the name of a GAL annotation environment created with the make.gal.env or the ReadExi functions. If galname is provided a NULL value, which is the default situation, a minimal GAL annotation environment is created based on the annotation contained in the ImageGene txt files.

Value

An AffyBatch object containing the raw expression data.

Warning

The image method of the AffyBatch object might not work properly when the galname argument of ReadExi has not been assigned.

Author(s)

Sylvain Gubian, Alain Sewer, PMP SA

See Also

make.gal.env, createAB.

Examples

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# The folder 'Exiqon' contains the file 'samplesinfo.txt' and  the corresponding raw data files in ImaGene format
## Not run: ebatch <- ReadExi(txtfile.path='Exiqon')
# If the GAL environment has already created by the function make.gal.env
## Not run: ebatch <- ReadExi(galenv='galenv', txtfile.path='Exiqon')