[BioC] hs133phsentrezg metadata

[Manhong Dai]

Hi Jim,

	In our custom cdf, some hits<1 probes would be used. For example, when
a probe has a hit with an allele of a snp, and the snp's another allele
has hits=1 match with genome, although the probe has no hit with genome
at all, we would use this probe and its genome location as a candidate
for all custom CDFs, although the portion of this kind of probes is
small.


	Our UG and ENTREZG custom CDF does have a rule that each probe must
only hit one genome location and one UG cluster.


	But in REFSEQ custom cdf, when a probe has match to a REFSEQ sequence,
but no match to genome at all. The probe would still be used because
REFSEQ is more reliable than genome.

	For example, probe 4 of
http://arrayanalysis.mbni.med.umich.edu/ps/ps_pb.jsp?p=NM_000019_at&c=Hs133P_Hs_REFSEQ_8  has no match to genome.


Best,
Manhong Dai


	
On Tue, 2006-10-17 at 14:46 -0400, James W. MacDonald wrote:
> 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
> 
> 
>