ae2bioc: Convert MAGE-TAB files from raw data into a Bioconductor...

In ebi-gene-expression-group/bioconductor-ArrayExpress: Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

Convert MAGE-TAB files from raw data into a Bioconductor object

Description

ae2bioc converts local MAGE-TAB files into a AffyBatch, an ExpressionSet or a NChannelSet.

Usage

ae2bioc(mageFiles, dataCols = NULL, drop = TRUE)

Arguments

mageFiles	A list as given from getAE function. Containing the following elements: rawFiles all the expression files to use to create the object. The content of the raw.zip MAGE-TAB file. sdrf the name of the sdrf file from MAGE-TAB. idf the name of the idf file from MAGE-TAB. adf the name of the adf file from MAGE-TAB. path is the name of the directory containing these files.
dataCols	by default, the columns are automatically selected according to the scanner type. If the scanner is unknown or if the user wants to use different columns than the default, the argument 'dataCols' can be set. For two colour arrays it must be a list with the fields 'R', 'G', 'Rb' and 'Gb' giving the column names to be used for red and green foreground and background. For one colour arrays, it must be a character string with the column name to be used. These column names must correspond to existing column names of the expression files.
drop	if TRUE and only one platform in series, the platform name will be dropped.

Value

An object of class AffyBatch, ExpressionSet or NChannelSet with the raw expression values in the 'assayData' of the object, the information contained in the sdrf file in the 'phenoData', the adf file content in the 'featureData' and the idf file content in the 'experimentData'.

If several array designs are used in the dataset, the output is a list with an object for each array design.

Author(s)

Ibrahim Emam

Maintainer: Jose Marugan <[e-mail]>

See Also

ArrayExpress, queryAE, getAE

Examples

# An example can be found in the help of the getAE function.

ebi-gene-expression-group/bioconductor-ArrayExpress documentation built on April 9, 2023, 6:39 a.m.