gene-locations

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Noemi Andor ▴ 100

@noemi-andor-4128

Last seen 10.2 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 • 1.2k views

ADD COMMENT • link updated 14.1 years ago by James W. MacDonald 67k • written 14.1 years ago by Noemi Andor ▴ 100

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Vincent J. Carey, Jr. 6.7k

@vincent-j-carey-jr-4

Last seen 9 weeks 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 >

ADD COMMENT • link 14.1 years ago Vincent J. Carey, Jr. 6.7k

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 1 minute 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

ADD COMMENT • link 14.1 years ago James W. MacDonald 67k

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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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