[Biopython] comparing micro array data

Tue Mar 16 16:38:43 UTC 2010

>
> t sounds a bit like you are doing array CGH, starting with an array that
> was raised to species X,

Yes

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.

I have 3 know species, X (the one that matches the array),B, C and about 8
arrays/samples and for each we know if a probe/sequence  matches a sequence
in the genome.

And several different unknown samples D,E,F.....

What to know if at any given sequence/probe does the unknown have that
sequence or some probability or the most likely to be different.

B,and C only help by allowing us to test our method.
I also have close mismatch data for the know, that is I know if there is a
single mismatch match and the distance of that mismatch from the center of
the sequence.

*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 10:03 AM, Leighton Pritchard <lpritc at scri.ac.uk>wrote:

> 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 are available (not to mention that arrays are being superseded by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 <e%3Alpritc at scri.ac.uk>       w:
> http://www.scri.ac.uk/staff/leightonpritchard
> gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405
>
>
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