[Biopython] comparing micro array data

[Vincent Davis]

>
> @Peter

For microarray work I would have to say using R/Bioconductor will

probably be more sensible for the very practical reason that they

have a much larger community using microarrays than Python does.

http://www.bioconductor.org/


I am working at getting up to speed with R and bioconductor. I ask the
question here as I got such a great answer for the last question I had and
thought if the tool was available in biopython then I would try it. I don't
know how this problem is normally solved.


<http://www.bioconductor.org/>

>

  *Vincent Davis
720-301-3003 *
vincent at vincentdavis.net
 my blog <http://vincentdavis.net> |
LinkedIn<http://www.linkedin.com/in/vincentdavis>


On Tue, Mar 16, 2010 at 9:15 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Tue, Mar 16, 2010 at 3:03 PM, Vincent Davis <vincent at vincentdavis.net>
> wrote:
> > So I am very new to this so please accept my ignorance on this subject.
> >
> > I have several micro array samples ~ 8 for each of 3 known genomes. So I
> > know which probes/sequences are a match and which have close matches. I
> > would like to identify which sequences exist in an unknown sample. The
> array
> > is custom and there is little to know overlap between probes.
> > What is the "standard" way of doing this? I don't care to know if a SNP
> is
> > present only if the sequence is present.
> > Is this standard available in biopython ?
>
> Hi Vincent,
>
> Biopython has only limited pairwise alignment built in - we normally just
> call specialised command line tools. In addition to classic microarray
> probe design tools, you *might* be able to exploit related tools for PCR
> primers or short read tools from next generation sequencing. However,
> these won't be specifically aware of microarray probe affinities and how
> to model them.
>
> For microarray work I would have to say using R/Bioconductor will
> probably be more sensible for the very practical reason that they
> have a much larger community using microarrays than Python does.
> http://www.bioconductor.org/
>
> Peter
>
> P.S. You can call R from Python, see http://rpy.sourceforge.net/
>