ExpressionSet R Objects

For many ArrayExpress experiments, an "ExpressionSet" object (e.g. E-MTAB-777.eSet.r) is available to download for direct loading into R.

screenshot showing ExpressionSet download link

ExpressionSet is the de facto object defined in the Bioconductor Biobase package for loading and manipulating microarray data in R. These objects are created using the ArrayExpress R package using default parameters. For each experiment, raw (un-normalized) data files are stored in the object as well as other metadata from its MAGE-TAB files, such as study, sample and gene metadata. Please refer to the package ArrayExpress package vignette for more details.

How to load ArrayExpress ExpressionSet objects in R

To load the E-MTAB-777.eSet.r object, download it, start R, and run the following command:

> load("path/to/E-MTAB-777.eSet.r")

This will create an ExpressionSet object named "study". If you plan to load multiple ExpressionSet objects, you should rename this object before loading the next one to prevent it from being overwritten. For example:

> mtab777eSet <- study

Not all ArrayExpress experiments have downloadable R objects. This is because some require running the ArrayExpress package R functions with user-set parameters. Instead, you can try creating the ExpressionSet yourself, by following the procedure outlined in the vignette.

Any problems?

Please report any problems with loading these files to iemam@ebi.ac.uk.