Hello I am working on a set of DNA methylation data generated from Nimblegen CHARM design. I used the CHARM scripts to generate some data with genomic region information, but could not get the gene symbols. Does anybody know how to generate gene symbol information from CHARM design? Thank you Xiaojin Li Staff Scientist Functional Genomic Core City of Hope [[alternative HTML version deleted]]

1) which array? does the probe design package for the (Nimblegen, IIRC) array have coordinates? 2) if so, have you tried turning the coordinates into a GenomicRanges object and using nearest(transcripts(TxDb.source.organism.build)) to find the closest feature? On Sat, Aug 4, 2012 at 1:45 AM, xiaojin li <lxj66228@hotmail.com> wrote: > > Hello > > I am working on a set of DNA methylation data generated from Nimblegen > CHARM design. I used the CHARM scripts to generate some data with genomic > region information, but could not get the gene symbols. Does anybody know > how to generate gene symbol information from CHARM design? > > Thank you > > Xiaojin Li > > Staff Scientist > Functional Genomic Core > City of Hope > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]