[BioC] hs133phsentrezg metadata

[James W. MacDonald]

Hi Manhong,

Manhong Dai wrote:
> Hi An,
> 
> 	Our custom CDF annotation package has only gene name for each probeset
> because we designed it this way.
> 
> 	A probeset's probes could have matches on different location or
> chromosomes, even some probes have no match on genome at all, but they
> belong to this probeset because they all have perfect match on the
> gene's sequence.

This doesn't make sense to me. How can a probe not match to the genome, 
yet have a perfect match to a gene's sequence?

I was also under the impression that the matching for the probes that 
remain in an MBNI cdf was first done to the genome, and those probes 
that didn't blast to the genome were discarded. From

http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/cdfreadme.htm

I get:

A probe must only hit one UniGene cluster and one genomic location

A probe must hit only one genomic location

Does this mean a probe that hits < 1 genomic location will be included? 
I assumed this meant a probe had to hit exactly one location.

Best,

Jim



-- 
James W. MacDonald, M.S.
Biostatistician
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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