getNormalisedAtlasExpression: Download normalised expression data for an Expression Atlas...

In ebi-gene-expression-group/bioconductor-ExpressionAtlas: Search, download and visualise datasets from EMBL-EBI Expression Atlas and Single-Cell Expression Atlas

Download normalised expression data for an Expression Atlas experiment

Description

This function downloads and returns normalised expression data for an Expression Atlas experiment, based on the ArrayExpress accession of the experiment.

Usage

    getNormalisedAtlasExpression( experimentAccession, normalisation )

Arguments

experimentAccession	ArrayExpress experiment accession e.g. "E-MTAB-4045"
normalisation	Normalisation method type e.g. "tpm", "fpkm", "cpm"

Value

A dataframe with expression values of the genes for each assay group. Entries are mean values of replicates.

Examples

    
    # Download the TPM Expression values for experiment E-MTAB-4045
    mtab4045_tpm <- getNormalisedAtlasExpression( "E-MTAB-4045", "tpm" )

    # See the entries available
    dim(mtab4045_tpm)
    # Prints out the following:
    # [1] 57147    45

    # Download the CPM Expression values for experiment E-MTAB-4045
    mtab4045_cpm <- getNormalisedAtlasExpression( "E-MTAB-4045", "cpm" )

    # See the entries available
    dim(mtab4045_cpm)
    # Prints out the following:
    # [1] 57147    275

ebi-gene-expression-group/bioconductor-ExpressionAtlas documentation built on July 4, 2025, 12:53 a.m.