Agilent Human Genome CGH 44K annotation
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Daniel Brewer ★ 1.9k
@daniel-brewer-1791
Last seen 8.0 years ago
Hi, I am looking for up to date annotation information for Agilent Human Genome CGH 44K microarrays (G4426B). There doesn't seem to be a bioconductor package for this array. Is this correct? What would be the best way to build up to date information for this microarray? Many thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}
Annotation Cancer CGH Annotation Cancer CGH • 826 views
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@sean-davis-490
Last seen 3 months ago
United States
On Mon, Sep 8, 2008 at 9:37 AM, Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> wrote: > Hi, > > I am looking for up to date annotation information for Agilent Human > Genome CGH 44K microarrays (G4426B). There doesn't seem to be a > bioconductor package for this array. Is this correct? What would be > the best way to build up to date information for this microarray? For CGH, the best way (in my opinion) to get up-to-date information is to align the probes to the reference genome. You could do this with blat (from UCSC), gmap, or using the Biostrings package. This will give you chromosome locations, obviously. Once you have done your segmentation analysis, you can find genes of interest using biomart or UCSC tables and overlaps. Sean
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