[BioC] AffyProbes and genome

[David Kipling]

Hi

The file Jim pointed you towards has a general location of the probeset (i.e.
the region in which the 16 or thereabout probes are based).

Somewhat more detail can be found in another Affymetrix file:

http://www.affymetrix.com/Auth/analysis/downloads/psl/HG_U95Av2.link.psl.zip

This now gives a bp position (in the very last column) for each of the 16 probes
in each probeset, rather than a single overall figure.  Note that some probeset
contain probes that map to different chrs, and thus there are multiple lines for
some probesets.

This figure for each probe may be enough for you;   I believe (someone please
correct me here!) that they are all 25mers, and if so then a single figure will
enable you to work out the beginning and end of each probe.   I have no idea
whether the figure given is the start, middle, or 13th basepair, but this is
something you could check quite quickly.

However...if you want a very nice overview of the mapping of individual probes
within a probeset to genomic and cDNA sequence information can I make a plug
here for ADAPT, from Crispin's lab?   Their paper is just out in Bioinformatics,
and the site is:

http://bioinf.picr.man.ac.uk/adapt/Welcome.adapt

This may help you.

Regards

David

Professor David Kipling
Department of Pathology,
School of Medicine,
Cardiff University,
Heath Park
Cardiff CF14 4XN

Email:  KiplingD at cardiff.ac.uk
Tel:  +44 29 2074 4847
fax:  +44 29 2074 4276
>>> Hrishikesh Deshmukh <d_hrishikesh at yahoo.com> 05/23/05 4:13 PM >>>
Thank you very much sir, just one more question. The
annotation file gives the "region" for each
probeset_Id but is it possible to get the start and
stop cooridnates 
for each of the 16 probes of a probeset_id.
For ex.
ProbeSet_ID| x|y| probeIndex| StartChrLoc| StopCHRLOC
1000_at      1 2  1           42545499     42545524
.
..
...
1001_at.........................
I wonder where can i find this information.

Thankyou very much again.
Hrishi



--- "James W. MacDonald" <jmacdon at med.umich.edu>
wrote:
> Hrishikesh Deshmukh wrote:
> > Pardon my ignorance.
> > How would i get the chromosomal locations written
> to a
> > text file for all the probes on HGU_95Av2. 
> 
> If all you want is the chromosomal locations in a
> text file, I would 
> simply download the annotation file from Affy, and
> delete all the other 
> columns.
> 
>
http://www.affymetrix.com/Auth/analysis/downloads/taf/HG_U95Av2_annot_csv.zip
> 
> This information is in the Genome Alignment column
> of the file.
> 
> Best,
> 
> Jim
> 
> 
> 
> 
> -- 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>

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