[BioC] gene-locations

Vincent Carey stvjc at channing.harvard.edu
Tue Oct 26 13:22:09 CEST 2010

Surely those who provide these annotation resources should be able to
clarify this, and should be encouraged to make the relevant connection
prominent in their distribution and documentation.  If this is
inconvenient, but you do have probe sequence and genomic coordinate
information for probes, you can take advantage of the
BSgenome.Hsapiens.UCSC.hg* packages along with Biostrings to check
which build corresponds to the information you have.  Let us know the

On Tue, Oct 26, 2010 at 3:21 AM, Noemi Andor <Noemi.Andor at campus.lmu.de> wrote:
> Hello,
> I have a question regarding the mapping of genes to their chromosomal locations.
> I'm using the expression data from affymetrix with probes attributed to the Hthgu133ahsrefseq - CDF files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/refseq.asp). On the other hand I'm using CNV-data from agilent (Agilent Human Genome CGH Microarray Kit 244K). I would like to assess the impact of CNV on expression - how could I find out on which genome assembly the mappings are based  (hg 17/18/19), i.e. if they are compatible?
> thank's
> Noemi
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