[BioC] AffyProbes abd genome

[James W. MacDonald]

Hrishikesh Deshmukh wrote:
> 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.

Well, you can get the probe interrogation position from the 
hgu95av2probe package and you could use this information to infer the 
start and stop coordinates for each of the probes. However, this will 
take a bit of work on your part to figure things out.

There may be a more straightforward way to get the start and stop 
coordinates, but offhand I can't think of one.

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