Skip to main content
Help us improve Python packaging – donate today!

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.

Installation

Option 1: Using pip

$ pip install pyaffy

Option 2: Cloning the GitHub repository

$ git clone https://github.com/flo-compbio/pyaffy.git
$ cd pyaffy
$ pip install -e .

Usage

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.

Release history Release notifications

This version
History Node

0.3.2

History Node

0.3.1

History Node

0.3.0

History Node

0.2.0

History Node

0.1.0

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
pyaffy-0.3.2.tar.gz (26.2 kB) Copy SHA256 hash SHA256 Source None Dec 6, 2016

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page