[BioC] probe lengths in annotation packages

[James W. MacDonald]

Hi Michael,

Michael Lawrence wrote:
> I have not been able to find a (easy) way to obtain from the annotation
> packages the lengths (in bases) of the probes (where applicable). Am I just
> missing something? There is start information on the chromosome but no way
> to calculate the ends without knowing the probe lengths.

Not sure what you are asking here. The annotation package contains no 
information about things that I would normally call probes. Instead, 
this package maps probesets to gene information (mostly), so you won't 
be able to get any probe information.

So when you say probes, what exactly do you mean? My definition is Affy 
centric - probes are 25-mers, 11 of which are used in the later versions 
of the 3' biased Affy chips to make up a probeset. If we are talking 
about the same thing, then the answer is 25.

If you are talking about something different, please clarify.

Best,

Jim


> 
> Thanks in advance,
> Michael
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
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