python script for robust multi-array average on microarray data

Question

I have tried google with no luck. I have seen some weak references to robust multi-array averaging done with python but no code. I am not so interested in reinventing the wheel. Any suggestions on a python module, script ....

If I could find a nice explanation or example of the algorithm I would write a python implementation to share.

If you are not sure what I am talking about you could look at this although this is not the definition. http://www.mathworks.com/access/helpdesk/help/toolbox/bioinfo/ref/gcrma.html

Answer 1

Even though this question was asked more than six years ago, when I asked myself the same question recently, I still couldn't find a good Python implementation of RMA. I therefore did a bunch of research into the methodology and wrote one myself:

• GitHub: https://github.com/flo-compbio/pyaffy

I also wrote an article about it that goes into some technical detail:

pyAffy: An efficient Python/Cython implementation of the RMA method for processing raw data from Affymetrix expression microarrays

Answer 2

You might want to consider using a python interface for R, which has gcrma packages for it. RPy is a module that allows you to use all R modules installed on your system. Bioconductor has a gcrma module for R. I couldn't find any modules for Python that do this.