[Genome] Affy U133 probe mappings missing?

[Rachel Harte]

John,

The knownToU133 table maps only the most overlapping probeset sequence to 
each Known Gene. The alignment should also be to the same strand for both 
the Known Gene and the U133 probeset sequence. The mapping is therefore 
one to one for mappings of Known Genes to U133 but each U133 probeset 
seqence can map to many Known Genes.
In your example, 117_at was chosen to be mapped to HSPA6 because the 
alignment of 117_at covers more of the region covered by aligning blocks 
in HSPA6 than 213418_at does.
I can easily generate a table that shows mappings of Known Genes to all 
probesets rather than just the one with the best overlap. If you would 
like to obtain that then please let me know.

I hope that this helps you. Please let us know if you have further 
questions.

Rachel

  On Tue, 10 Oct 2006, John Major 
wrote:

> I'm working with U133A Affy chips, and would like to use the UCSC known
> gene mappings for each probe name.
>
> I am using the hg17 assembly, and noticed that a probe was missing(and
> possibly more) from the knownToU133 table (But,  it is listed in the
> AffyU133 table?).
> Probe 117_at maps to HSPA6, and is in both tables above. The probe
> 213418_at should also map to that same gene, but is only listed in the
> u133 table above and not in the known gene mapping table?
>
> Were probes that were excluded from the knownToU133 table excluded b/c
> they did not actually align to the gene?
>
> Thanks,
> John
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>

-- 
Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu