Expression Atlas data in R
For differential expression 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.
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.
Load the object you downloaded into your R session, e.g.:
load( "/path/to/E-GEOD-38400-atlasExperimentSummary.Rdata" )
- SummarizedExperiment (RNA-seq experiments)
- ExpressionSet (1-colour microarray experiments)
- MAList (2-colour microarray experiments)
How to use it
If you have not already installed this package, do this by running the following two commands:
source( "http://bioconductor.org/biocLite.R" )
biocLite( "GenomicRanges" )
Now load the package into your R session:
library( GenomicRanges )
For more details about using using this package please see the documentation.
Data from an RNA-seq experiment is contained in a single SummarizedExperiment object in the SimpleList you have loaded.
The SummarizedExperiment object is stored under the name "rnaseq", so you can assign it to a new variable like this:
summarizedExperiment <- experimentSummary$rnaseq
The 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.
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.
You can access each ExpressionSet via its array design accession, by typing
expressionSet <- experimentSummary[[ "A-AFFY-18" ]]
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 ) )
Two-colour microarray data
Data from a two-colour microarray experiment is stored in one or more MAList objects. As for ExpressionSet objects, there is one MAList per array design used in the experiment. This means you can access each MAList object via its ArrayExpress array design accession.
Each MAList object contains the following:
- Vector of probe names, in the genes element.
- Matrix of log2(fold-change) values, in the M element.
- Matrix of LOESS normalized average intensities, in the A element.