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EBIArrayExpressQuery HelpFiles for Download

File Downloads Available from ArrayExpress

This page describes what information is available for download from the FTP site for the ArrayExpress microarray archive. Most files are now in MAGE-TAB format.

Descriptions and data for all public experiments and array designs are available for download from the ArrayExpress FTP site. The FTP site is organized as follows:

ftp.ebi.ac.uk/pub/databases/microarray/data
Folder: array Descriptions of all array designs in ArrayExpress.
Folder: experiment Data files and meta data (sample descriptions, protocols, etc) for all experiments in ArrayExpress.

Experiments and array designs in the subdirectories are grouped by the four letter codes in their accession numbers.

For example:

 

Note: ArrayExpress Bioconductor package. The naming convention for the raw and processed data file archive has changed (Oct 2009). You must use the latest version of the ArrayExpress package to access them.

 

File types in experiment directories

The data files and experiment information are available in a number of different formats. These formats and their uses are described here:

 

File extension Description Format/Usage
.idf.txt and .idf.xls Top level information about the experiment including title, description, submitter contact details and protocols. MAGE-TAB format
Use with .sdrf and data files from .raw.zip and .processed.zip
.sdrf.txt and .sdrf.xls Information about the samples, the relationships between the samples, extracts, labeled extracts, hybridizations, factor values and data files. MAGE-TAB format
Use with .idf and data files from .raw.zip and .processed.zip
.2columns.txt and .2columns.xls A table listing the samples, experimental factor values, and the corresponding data files. This file will be replaced by the MAGE-TAB IDF and SDRF. A subset of the information from .sdrf
Use with data files from .raw.zip and .processed.zip
.raw.1.zip All raw data files as named in the .sdrf and .2columns description files. CEL files are provided for Affy experiments. Other files are in generic tab delimited text format. Large data sets are split into a number of different archives .raw.1.zip, .raw.2.zip etc. Use with MAGE-TAB .sdrf and .idf files, or with .2columns file
.processed.1.zip All processed data files as named in the .sdrf description file. Files are in generic tab delimited text format. Each processed file may contain data from 1 or more hybs. Large data sets are split into a number of different archives .processed.1.zip, .processed.2.zip etc. Use with MAGE-TAB .sdrf and .idf files, or with .2columns file
.biosamples.png
.biosamples.svg
.biosamples.map 		A diagram of the sample relationships in .png or .svg format. The graph represents the processing steps for each sample, each edge represents a protocol that has been applied. Typically the graph shows, from left to right: BioSource-> BioSample-> Extract-> LabeledExtract->Hybridization->Raw Data. Visual representation of the experiment design
.mageml.gz or
.mageml.tar.gz or
.mageml.tgz or
.mageml.zip 		The MAGE-ML containing all information about the experiment and the data matrices as loaded into ArrayExpress. MAGE-ML format
Use with CEL files from .cel archive if available.
.cel.tar.gz or
.cel.tgz or
.cel.zip 		Affymetrix CEL files with original names.
The same files with different names are available in the .raw archive for non MAGE-ML users.		 For use with MAGE-ML from .mageml archive.
.biosamples.xls Information about all biological samples and how the samples have been processed before hybridization. This file will be replaced by the .sdrf file
.hybs.xls Information about hybridizations in the experiment including references to hybridization protocols, array designs, factor values and biological samples. This file will be replaced by the .sdrf file

Processed and raw data files can also be downloaded though the link http://www.ebi.ac.uk/microarray-as/aer/download/mageml/<file> where the filename is the same as in the FTP site. For example:
http://www.ebi.ac.uk/microarray-as/aer/download/mageml/E-MEXP-43.raw.1.zip

Any further questions, please see our FAQ.

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