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

View source: R/ae2bioc.r

ae2biocR Documentation

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


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


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



A list as given from getAE function. Containing the following elements:


all the expression files to use to create the object. The content of the MAGE-TAB file.


the name of the sdrf file from MAGE-TAB.


the name of the idf file from MAGE-TAB.


the name of the adf file from MAGE-TAB.


is the name of the directory containing these files.


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.


if TRUE and only one platform in series, the platform name will be dropped.


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.


Ibrahim Emam

Maintainer: Jose Marugan <>

See Also

ArrayExpress, queryAE, getAE


# 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.