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orange-bioinformatics / docs / rst / reference / arrayexpress.rst

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Array Express (:mod:`arrayexpress`)

Access the ArrayExpress web services and database.

ArrayExpress is a database of gene expression experiments that you can query and download.

Retrieve the object representing experiment with accession E-TABM-25

>>> from Orange.bio import arrayexpress
>>> experiment = ArrayExpressExperiment("E-TABM-25")
>>> print experiment.accession
E-TABM-25
>>> print experiment.name
Transcription profiling of aging in the primate brain
>>> print experiment.species
['Pan troglodytes']
>>> print experiment.files
[{'kind': ...
>>> # Retrieve the data matrix for experiment 'E-MEXP-2917'
>>> experiment = ArrayExpressExperiment("E-MEXP-2917")
>>> table = experiment.fgem_to_table()

Low level Array Express query using REST services:

>>> from Orange.bio import arrayexpress
>>> arrayexpress.query_experiments(accession='E-MEXP-31')
{u'experiments': ...

>>> arrayexpress.query_experiments(keywords='gliobastoma')
{u'experiments': ...

>>> arrayexpress.query_files(accession='E-MEXP-32', format="xml")
<xml.etree.ElementTree.ElementTree object ...

Note

Currently querying ArrayExpress files only works with the xml format.

Interface

Low-level querying with REST