ArrayExpress: R objects from ArrayExpress collection

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

R objects from ArrayExpress collection

Description

ArrayExpress produces an AffyBatch, an ExpressionSet or a NChannelSet from a raw dataset from the ArrayExpress collection of the Biostudies database. ArrayExpress needs an Internet connection.

Usage

ArrayExpress(accession, path = tempdir(), save = FALSE, dataCols = NULL, drop = TRUE)

Arguments

accession	an ArrayExpress experiment identifier.
path	the name of the directory in which the files downloaded on the ArrayExpress repository will be extracted. The default is the current directory.
save	if TRUE, the files downloaded from the database will not be deleted from path after executing the function.
dataCols	by default, for the raw data, 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

The output is an object of class AffyBatch or 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 in the featureData and the idf file content in the experimentData.

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

Author(s)

Audrey Kauffmann, Ibrahim Emam

Maintainer: Jose Marugan <[e-mail]>

See Also

queryAE, getAE, ae2bioc, getcolproc, procset

Examples

ETABM25.affybatch = ArrayExpress("E-TABM-25")
print(ETABM25.affybatch)
sampleNames(ETABM25.affybatch)
colnames(pData(ETABM25.affybatch))

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