Expression Atlas < EMBL-EBI

Expression Atlas data in R

For microarray and RNA-seq experiments in Expression Atlas, you can download a file containing the expression data and meta-data that you can load into R. Click the R button on the top-right of any differential experiment page to download one.

Experiment page download button screenshot

How to load an Atlas experiment summary in R

Start an R session on your computer. For details on how to get and use R, please see the documentation on the R project website.

New R session screenshot

Required packages

In order to use the object you will need to install a few packages from Bioconductor. These are:

If you have not already installed these packages, do this by running the following two commands:

source( "http://bioconductor.org/biocLite.R" )

biocLite( c( "S4Vectors", "IRanges", "GenomicRanges", "SummarizedExperiment" ) )

For more details about using using this package please refer to Bioconductor.

Load the Expression Atlas data

Load the object you downloaded into your R session, e.g.:

load( "/path/to/E-GEOD-38400-atlasExperimentSummary.Rdata" )

Load Atlas Rdata object screenshot

This has created an object called experimentSummary. This object is a SimpleList object (see the S4Vectors package). Each element is one of three Bioconductor objects:

How to use it

RNA-seq data

Data from an RNA-seq experiment is contained in a single RangedSummarizedExperiment object in the SimpleList you have loaded.

The RangedSummarizedExperiment object is stored under the name "rnaseq", so you can assign it to a new variable like this:

rSumExp <- experimentSummary$rnaseq

RangedSummarizedExperiment screenshot

The RangedSummarizedExperiment object contains the following:

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

For more information on how to use a RangedSummarizedExperiment object, please see the documentation from Bioconductor.

One-colour microarray data

Data from a one-colour, or single-channel, microarray experiment is stored in potentially multiple ExpressionSet objects in the SimpleList summary you have loaded. There is one ExpressionSet per array design used in the experiment. The ExpressionSets are indexed by the ArrayExpress accession of the array design used.

Multiple array design names screenshot

You can access each ExpressionSet via its array design accession, by typing e.g. expressionSet <- experimentSummary[[ "A-AFFY-18" ]]

ExpressionSet screenshot

Each ExpressionSet object contains the following:

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

For more information on how to use an ExpressionSet object, please see the documentation from Bioconductor.