Dear All, I have 4000 genes (HG_U94Av2, tab separated) files with signal intensities, how can i map the position of each gene on human chromosomes and if possible plot signal intensities, log and raw. This is my first stab at this, so kindly pardon my ignorance on this issue. Thanks, Hrishi

It is pretty simple, find the annotation package for your chip (your name is not right though, I think) and there is a CHRLOC table in it, with chromosome locations. You only need to do more if you want to make use of the plotting functions (in geneplotter, for example) Robert eg library(hgu95av2) ?hgu95av2CHRLOC should get you started - and as others have said, the vignettes should give you lots of information, but let us know if they are not clear (or our new book) Hrishikesh Deshmukh wrote: > Dear All, > > I have 4000 genes (HG_U94Av2, tab separated) files > with signal intensities, how can i map the position of > each gene on human chromosomes and if possible plot > signal intensities, log and raw. > > This is my first stab at this, so kindly pardon my > ignorance on this issue. > > Thanks, > Hrishi > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Dear Hrishikesh, I don't know how to do it in Bioconductor, but Onto-express is a web-tool that maps a gene list to chromosomes. You can find the web-site in a Google search. Best wishes, Rich > Dear All, > > I have 4000 genes (HG_U94Av2, tab separated) files > with signal intensities, how can i map the position of > each gene on human chromosomes and if possible plot > signal intensities, log and raw. > > This is my first stab at this, so kindly pardon my > ignorance on this issue. > > Thanks, > Hrishi > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "42 is the answer. Dylan got it wrong. 'Blowin' in the wind' is not the answer. It isn't even a number' " - Rose Friedman, age 9

On 11/11/05 9:25 AM, "Hrishikesh Deshmukh" <d_hrishikesh at="" yahoo.com=""> wrote: > Dear All, > > I have 4000 genes (HG_U94Av2, tab separated) files > with signal intensities, how can i map the position of > each gene on human chromosomes and if possible plot > signal intensities, log and raw. Here is a vignette for the 'annotate' package that answers many of your questions. Ironically, it is actually based on hgu95av2. http://www.bioconductor.org/repository/devel/vignette/chromLoc.pdf Sean

I think the general sequence would be: 1) read in the data files using something like read.delim() 2) make sure you have the hgu95av2 meta data package installed 3) use something like buildChromLocation() from the annotation package to associate probe ids with genomic location 4) use something like geneplotter, chromViz, or the ideogram package to plot the data. The specifics of these packages vary, but they mostly take the same types of data structures -kyle ## ## Example code: Do not run ## my_data <- read.delim("my_file") ## lets say there are columns called RAW and ID in the file raw_data <- my_data[,"RAW"] names(raw_data) <- my_data[,"ID"] ## do some plots library(hgu95av2) cL <- buildlChromLocation("hgu95av2") library(ideogram) mideogram(raw_data,cL) > From: Hrishikesh Deshmukh <d_hrishikesh at="" yahoo.com=""> > Date: Fri, 11 Nov 2005 06:25:26 -0800 (PST) > To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] Gene Mapping on Chrosmosomes > > Dear All, > > I have 4000 genes (HG_U94Av2, tab separated) files > with signal intensities, how can i map the position of > each gene on human chromosomes and if possible plot > signal intensities, log and raw. > > This is my first stab at this, so kindly pardon my > ignorance on this issue. > > Thanks, > Hrishi > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > This email message, including any attachments, is for the so...{{dropped}}

Hi... I find the package ChromoViz very usefull for this issue homepage: http://www.snubi.org/software/ChromoViz/ good luck morten >Dear All, > >I have 4000 genes (HG_U94Av2, tab separated) files >with signal intensities, how can i map the position of >each gene on human chromosomes and if possible plot >signal intensities, log and raw. > >This is my first stab at this, so kindly pardon my >ignorance on this issue. > >Thanks, >Hrishi > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > >