Affymetrix Microarray Analysis In Python

Question

[Will]

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.

Answer 1

[Leandro Lima]

http://biopython.org/DIST/docs/api/Bio.Affy.CelFile-pysrc.html

Answer 2

[popantrop]

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 :)

[popantrop]

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

Answer 3

[Leandro Lima]

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/

[Will]

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).

[Ben]

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).

[Neilfws]

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.