ArrayExpress Tab2MAGE / News: Recent posts

The GEOImport package (version 1.0) has now been released as part of the ArrayExpress Tab2MAGE project. This package provides tools to import Affymetrix experiments deposited with the NCBI GEO database, process them with an information extraction ("text mining") module, and generate a reannotated Tab2MAGE document as output. Work is continuing on support for other microarray platforms. The source code can be downloaded from the following web page:... read more

An early release (v0.6) of the mage2tab conversion script has been released as part of the Tab2MAGE project. The script is being developed to convert MAGE-ML documents to the new MAGE-TAB format. This package is maintained by Junmin Liu at the University of Pennsylvania. Release notes and up-to-date information can be obtained here:

https://www.cbil.upenn.edu/magewiki/index.php/mage2tab

The package can be downloaded here:... read more

A set of mappings from Tab2MAGE to MAGE-TAB have now been released as part of the ArrayExpress Tab2MAGE project. These mappings have been created by Faisal Rezwan in the EBI Microarray Informatics group. Faisal is also working on a stand-alone Tab2MAGE to MAGE-TAB converter.

The mappings document can be downloaded in RTF and PDF formats here:

https://sourceforge.net/project/showfiles.php?group_id=120325&package_id=222159

Tab2MAGE version 1.8.5 has now been released. This bugfix release is a recommended upgrade for all users of the stable version. Included is a set of updated array design download URLs for connection to ArrayExpress, which will fix recent problems with connections to the ArrayExpress web interface. In addition, support for ArrayVision data files has been extended with this release.

It is anticipated that this will be the final release of the 1.8 series; a 1.9.0 development version should be released within the next month or so.... read more

The ADFchecker perl script and database patterns file (version 6.2) have now been released as part of the ArrayExpress Tab2MAGE project. This script is used by the ArrayExpress database curators to check all incoming array designs submitted in ADF form for validity. An online version of the script can be accessed here:

http://www.ebi.ac.uk/cgi-bin/microarray/ADF_checker_page.pl

The scripts may now be downloaded for local use from this web page:... read more

Tab2MAGE version 1.8.3 has now been released as a stable package. The main changes since version 1.7.4 are as follows:

tab2mage.pl - native file format encoding has been enabled for Affymetrix and Nimblegen data files; spreadsheet parsing has been made more reliable, particularly with regard to protocol text; greater flexibility has been added to the parsing of a variety of raw data file formats.

expt_check.pl - new reports are now generated, summarizing factor values and sample annotation for MIAMExpress submissions.... read more

Tab2MAGE is a data submission and MAGE-ML creation tool maintained by the curators at the ArrayExpress microarray repository database. Version 1.7 marks the formal separation of stable and development releases of this package. It is anticipated that users wishing to use Tab2MAGE in a production environment should use the stable release (currently at version 1.6.4). Bug fixes will be applied to both stable and development releases. New features will appear first in the developmental release, and will be migrated to the stable version after a period of testing. Tab2MAGE is available at http://tab2mage.sourceforge.net

Tab2MAGE is a tool to create MAGE-ML from microarray data files linked to an annotation spreadsheet. The 1.5.1 release of Tab2MAGE includes a set of Perl modules which may be used by developers to parse Affymetrix format data files. Both the newer XDA/GCOS and the historic GDAC formats are supported. The Tab2MAGE package includes full documentation of the Affymetrix parsing API. The API has now stabilized, and the behaviour of the included method calls is not expected to change any further. An example script using the modules, 'parse_affy.pl', is included with the distribution.