Question: Affymetrix Microarray Analysis In Python
1
gravatar for Will
6.5 years ago by
Will4.5k
United States
Will4.5k wrote:

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 • 6.5k views
ADD COMMENTlink modified 2.5 years ago by popantrop30 • written 6.5 years ago by Will4.5k
2
gravatar for Leandro Lima
6.5 years ago by
Leandro Lima920
San Francisco, CA
Leandro Lima920 wrote:

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

ADD COMMENTlink written 6.5 years ago by Leandro Lima920
2
gravatar for popantrop
2.5 years ago by
popantrop30
popantrop30 wrote:

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 :)

ADD COMMENTlink written 2.5 years ago by popantrop30

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

ADD REPLYlink written 2.5 years ago by popantrop30
0
gravatar for Leandro Lima
6.5 years ago by
Leandro Lima920
San Francisco, CA
Leandro Lima920 wrote:

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/

ADD COMMENTlink written 6.5 years ago by Leandro Lima920

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).

ADD REPLYlink written 6.5 years ago by Will4.5k
4

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).

ADD REPLYlink written 6.5 years ago by Ben2.0k
4

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.

ADD REPLYlink written 6.5 years ago by Neilfws48k
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