ArrayExpress: R objects from ArrayExpress database

Description

ArrayExpress produces an AffyBatch, an ExpressionSet or a NChannelSet from a raw dataset from the ArrayExpress 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.

Examples

Run this code

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

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