[Biopython] comparing micro array data

[Leighton Pritchard]

Hi Vincent,

On 16/03/2010 Tuesday, March 16, 15:30, "Vincent Davis"
<vincent at vincentdavis.net> wrote:

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

Peter's suggestion is a good one, in general.  Biopython is lacking in
support for microarray analysis - not least in part because there's already
an adaptor to R, from which the mature and powerful Bioconductor libraries
are available (not to mention that arrays are being superseded by
sequencing, so now might not be the time to put too much effort in to that
;)).  If you've got microarray issues, a Bioconductor mailing list might be
a better first port of call.

>> 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 ?

It's not very clear to me what the problem is, from your description here.
It sounds a bit like you are doing array CGH, starting with an array that
was raised to species X, and you then have eight sets of array results (this
wouldn't be two samples with three replicates, and a single sample with two
replicates, would it?) from known species A, B, and C.  Then it seems like
you have a sample from species D, and you want to know - perhaps from the
array hybridisation data, perhaps from the genome sequence, it's hard to
tell - possibly one of two things: which probes will bind to species D; or
how many genes from species D are similar to those in species X.  These two
questions would require quite different approaches; can you be clearer?

Cheers,

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
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