Hi All, We want to use geneplotter/geneGraph to map the gene expression on each chromosome for opossum/platypus/or any other genome which not supported by bioconductor genome datasets. We had mapping position for each gene on each chromosome. How do we write the data for using geneplotter/geneGraph? For example, buildChromLocation doesn't support these genomes, how do we build the similar annotation data as BioC did for human/mouse? Thanks, Zhuo-Cheng [[alternative HTML version deleted]]

Dear Zhuo-Cheng, I am currently having a similar problem using the GenomeGraphs package. It seems that as long as you are doing mainstream, like human, mouse, things are fine, very easy to work with these packages, but as soon as you try something that is a little more uncommon, you are immediately out of luck, because you either need a genome in a certain database or a custom made dataset like the hgu-something. Also, there seems to be almost no documentation for this task. So I think there is definitely room for improvement here. Thanks to kind help from the list I figured out how to read in a GFF file using rtracklayer. Now I am trying to make a plot of the genome imported from a file using genomegraphs. If I succeed, I can share the results, although I am no sure if that visualization is what you need. Best Michael Am 31.07.2009 um 02:28 schrieb zhuocheng Hou: > Hi All, > > We want to use geneplotter/geneGraph to map the gene expression on > each > chromosome for opossum/platypus/or any other genome which not > supported by > bioconductor genome datasets. We had mapping position for each gene > on each > chromosome. How do we write the data for using geneplotter/geneGraph? > > For example, buildChromLocation doesn't support these genomes, how > do we > build the similar annotation data as BioC did for human/mouse? > > Thanks, > Zhuo-Cheng > > [[alternative HTML version deleted]] > > _______________________________________________ > 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