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pyAffy: Processing raw data from Affymetrix expression microarrays in Python.

Project description

pyAffy is a Python/Cython implementation of the RMA algorithm for processing raw data from Affymetrix expression microarrays. For a detailed discussion of this implementation, see the pyAffy PeerJ preprint. For a list of changes, see the changelog.


Option 1: Using pip

$ pip install pyaffy

Option 2: Cloning the GitHub repository

$ git clone
$ cd pyaffy
$ pip install -e .


The rma function expects two parameters: A custom CDF file (from the Brainarray web site) and an ordered dictionary (collections.OrderedDict) with sample names as keys and corresponding CEL files as values.

The rma function returns a list of genes, a list of samples, and an expression matrix (of type numpy.ndarray), in that order.

from pyaffy import rma
# for documentation of the rma function, try:
# help(rma)
genes, samples, X = rma(cdf_file, sample_cel_files)

A small example with real code is available in the pyaffy-demos repository.

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