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.

Is 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

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.

Answer 2

I am a biologist working in genomics and contributed to 5-6 microarray projects. I am also quite fluent in Python and can make do pretty well in R.

Python is a great language, but as of now, I am aware of no module that would suite your request easily. R, on the other hand, offers a large gamut of packages for microarray analysis.

Given how microarray data analysis is driven by medical use of standard microarray chips/technologies, biological research has had to use custom developed (mostly R) packages for analysis purposes. Unfortunately, I believe that this situation has left a not so interesting niche for microarray data analysis in more full-fledged programming languages, which are not as appreciated by the crowd of research students.

Hope you do find a python alternative, in which case, please let us know!

Cheers