Comments on: Automated retrieval of expression data with Python and R http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/ Fri, 24 May 2013 09:34:41 +0000 hourly 1 http://wordpress.com/ By: Chris Plaisier http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-198 Sat, 04 Sep 2010 00:00:52 +0000 http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-198 Just FYI there is a great download of the meta information from GEO @ this web site:

http://gbnci.abcc.ncifcrf.gov/geo/

Like your python implementation. ;-)

Peace,
Chris

]]> By: Nicolas http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-161 Thu, 25 Mar 2010 09:30:42 +0000 http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-161 alright, thanks i ll mail the dev list then.

]]> By: Brad Chapman http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-160 Wed, 24 Mar 2010 13:08:11 +0000 http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-160 Nicolas;
That sounds great and would definitely be useful for Biopython. Contributions are very welcome. The best plan is to fork the GitHub trunk:

http://github.com/biopython/biopython/

For organizing, testing and documenting the code, useful tips are here:

http://biopython.org/wiki/Contributing

Feel free to send along any questions or progress reports to the Biopython mailing lists.

Brad

]]> By: Nicolas Rapin http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-159 Mon, 22 Mar 2010 10:15:51 +0000 http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-159 Hi,

This is indeed a very nice little script you have made here.
Actually, I wrote a similar one based on yours, that does not depend on Rpy2 and the GEOquery package. and is purely in python. could that be something for BioPython?

]]> By: Paul http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-146 Tue, 09 Feb 2010 20:43:30 +0000 http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-146 Hey man just saying thanks for the great article it was very useful to what I’m doing at the moment.

]]> By: lgautier http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-144 Sun, 07 Feb 2010 15:44:48 +0000 http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-144 Similar issue for me. I had something to post off-blog, but had a hard time finding an email address.

]]> By: Sri Kosuri http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-142 Tue, 02 Feb 2010 20:22:04 +0000 http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-142 Hi Brad,

I’m a post-doc in George Church’s lab at Harvard; I’ve been trying to contact you using your address in your code repositories (the synbio package) to no avail. Could you drop me a line when you get a chance.

Thanks.

]]> By: Brad Chapman http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-138 Wed, 06 Jan 2010 12:49:55 +0000 http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-138 Laurent;
Thanks for the more pythonic example — that’s really useful. Personally, I go back and forth on whether I prefer that way or the code snippets approach. Moving into snippets has been helping me practice my R skills, but does require the reader to feel comfortable with both Python and R syntax.

Thanks also for all your hard work on rpy. 2.1.0 is awesome; I love the ggplot2 integration.

Brad

]]> By: Laurent http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-137 Wed, 06 Jan 2010 07:17:32 +0000 http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-137 Once more an interesting demonstration of how some tools can be bridged.

This is also making me notice that some features in rpy2 are probably not as well documented as they should.

The use of a snippets of R code is perfectly fine,
however the option to move the code logic to Python exists (can make it easier for debugging with pdb,
allows the use of anonymous R variable that do not stay in R’s “globalenv”).

(note: the following code is taking advantage of the features in rpy2-2.1.0, but the same idea could be used with 2.0.x…)

from rpy2.robjects.packages import importr
utils    = importr("utils")
geoquery = importr("GEOquery")
rjson    = importr("rjson")

def _write_gsm_map(self, gsm_id, 
                   meta_file, table_file):
    """Retrieve GEO expression values using Bioconductor, saving to a table and a jason file.
    """
    gsm = geoquery.getGEO(gsm_id)
    utils.write_table(geoquery.Table(gsm),
                      file = table_file,
                      sep = "\t",
                      row_names = False,
                      col_names = True)
    json_data = rjson.toJSON(geoquery.Meta(gsm))
    fh = file(meta_file, "w")
    fh.write(json_data)
    fh.close()

One can as also return “json_data” rather than save it into a file then read it immediately from the file.

L.

]]> By: Nick http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-136 Tue, 05 Jan 2010 13:44:27 +0000 http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/#comment-136 Brad,

Good to see you’re still posting. I’ve found some of your code to be quite useful. Thanks!

- Nick

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