gene-locations
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Noemi Andor ▴ 100
@noemi-andor-4128
Last seen 9.6 years ago
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
cdf cdf • 1.0k views
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@vincent-j-carey-jr-4
Last seen 16 days ago
United States
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 outcome. 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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@james-w-macdonald-5106
Last seen 8 hours ago
United States
Hi Noemi, On 10/26/2010 3:21 AM, Noemi Andor 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? http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13. 0.0/version.html Best, Jim > > thank's > > Noemi > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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Thank's! Noemi ________________________________ Von: James W. MacDonald <jmacdon@med.umich.edu> An: Noemi Andor <noemi.andor@campus.lmu.de> CC: bioconductor@stat.math.ethz.ch Gesendet: Dienstag, den 26. Oktober 2010, 6:10:14 Uhr Betreff: Re: [BioC] gene-locations Hi Noemi, On 10/26/2010 3:21 AM, Noemi Andor 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/1 3.0.0/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? http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13. 0.0/version.html Best, Jim > > thank's > > Noemi > > _______________________________________________ Bioconductor mailing > list Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues [[alternative HTML version deleted]]
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