getAtlasExperiment: Download data for an Expression Atlas experiment
In mkeays/ExpressionAtlas: Download datasets from EMBL-EBI Expression Atlas

Description Usage Arguments Value Examples

This function downloads and returns a SimpleList object representing a single Expression Atlas experiment, based on the ArrayExpress accession of the experiment.

1	getAtlasExperiment( experimentAccession )

experimentAccession

ArrayExpress experiment accession e.g. "E-GEOD-11175"

A SimpleList object representing a single Expression Atlas experiment. The SimpleList contains one entry per platform used in the experiment. For sequencing experiments, there is a single entry in the list. For microarray experiments, there is one entry per array design used. Currently Expression Atlas does not support multi-technology (e.g. microarray and RNA-seq) experiments.

For a single-channel microarray experiment, each entry of the list is an ExpressionSet object. For a sequencing experiment, the single entry is a SummarizedExperiment object. Please refer to the relevant documentation on these classes for more information about them.

RNA-seq data

Each SummarizedExperiment object contains the following:

Matrix of raw counts (not normalized), in the assays slot, in a counts element.
Sample annotations, in the colData slot.
Brief outline of methods, from QC of FASTQ files to production of raw counts, in the exptData slot.

Single-channel microarray data

Each ExpressionSet object contains the following:

Matrix of normalized intensity values, in the assayData, accessed via: exprs( expressionSet )
Sample annotations, in the phenoData, accessed via: pData( expressionSet )
Brief outline of normalization method applied, in the experimentData slot, accessed via: preproc( experimentData( expressionSet ) )

    
    # Download the experiment summary for E-GEOD-11175
    geod11175 <- getAtlasExperiment( "E-GEOD-11175" )

    # See the entries available (in this case array design accessions)
    names( geod11175 )
    # Prints out the following:
    # [1] "A-AFFY-126"

    # Get the only ExpressionSet object from this experiment.
    eset <- geod11175[[ "A-AFFY-126" ]]