This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Affymetrix Microarray Analysis In Python

I was wondering if anyone knew of some python projects for microarray analysis, specifically reading in Affy Cel files. I know about An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators and the other projects to link R and Python. I'd love a native python project if possible.

python microarray
• 14,484 views • link
updated by popantrop • popantrop • written by Will Will

3 answers

I have written a parser in pure python 3, which can deal with Affymetrix CEL files, version 4. This version is difficult to parse, because it's binary and poorly documented. Data produced from Human Exon Chip should be compatible with this parser.

If you're interested in parsing other versions of CEL files, give me a shout and I'll see what I can do :)

• 0 views • link
written by popantrop • popantrop

Actually, I've just checked and the code works also with python2

• 0 views • link
written by popantrop • popantrop

Hello Will. I think these link can be useful.

http://stats.stackexchange.com/questions/1595/python-as-a-statistics-workbench

http://www.astro.cornell.edu/staff/loredo/statpy/

• 0 views • link
written by Leandro Lima Leandro Lima

Thanks for the links but I'm really looking for something for reading the Cel files. I already know the vast number of stats projects in Python (that's exactly why I want to read the cel files in without doing a dance with R modules).

• 0 views • link
written by Will Will

You really don't have to do much of a dance, just by skimming the Bioconductor documentation you could copy a few lines of R that will read your CELs, normalise, correct etc. and export to a plaintext format which you could then look at in Python (personally I'd stick with R throughout but I feel that'd be a much harder sell to yourself if you're proficient in Python and have no R experience).

• 0 views • link
written by Ben Ben

Agree with these points. Sometimes it's better to invest effort learning an existing tool (in this case R/Bioconductor) than reinventing the wheel, just for the sake of using your pet language.

• 0 views • link
written by Neilfws Neilfws

Log in to answer this question.

More posts like this