Hi, I have a set of genes and its chromosomal physical position in a text file. I want to view those genes in the chromosome using R package GenePlotter. Could any one please tell how to view this. Thanks in advance. Yours sincerely, S.Mahalakshmi [[alternative HTML version deleted]]

Hi S.Mahalakshmi, On 7/6/2010 1:11 AM, mahalakshmi sivamani wrote: > Hi, > > I have a set of genes and its chromosomal physical position in a text file. > I want to view those genes in the chromosome using R package GenePlotter. > Could any one please tell how to view this. Have you looked at the vignettes for this package? What have you tried so far? You will get much more traction if you show that you have at least made an attempt to figure things out for yourself, and show where things went wrong. Best, Jim > > Thanks in advance. > > > Yours sincerely, > > S.Mahalakshmi > > [[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 -- 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

Hi, First off, please don't take conversations off-list. The archives are intended to be a resource for people to search, and if the conversation becomes private that function ceases to exist. On 7/7/2010 3:15 AM, mahalakshmi sivamani wrote: > Hi, > > I visualized the chromosome and genes of the hgu133a array with > geneplotter package using the following commands, > > *library(annotate) > library(geneplotter) > library(hgu133a) > newChrom <- buildChromLocation("hgu133a") > cPlot(newChrom) Well you obviously have read the vignette, but evidently didn't understand that there is just one step remaining. So here is an example: library(geneplotter) library(hgu133a.db) ## note that if you still have a package called hgu133a, then you seriously need to update your R and BioC to the release versions. newChrom <- buildChromLocation("hgu133a") cPlot(newChrom, c(1:22, "X","Y")) ## Unless you like the extra clutter, I prefer to subset to non-random chromosomes ## now fake up some genes - you of course would use the 100 that you are interested in gns <- sample(Lkeys(hgu133aSYMBOL), 100) cColor(gns, "red", newChrom) And that, I believe is what you wanted. Best, Jim > > *I have a list of 100 genes of hgu133a microarray type and its physical > position. I want to visualize and differentiate those genes from other > genes of the chromosome. > > For Eg, > > image.bmp > > I have to visualize my genes like the above picture. How can I proceed > hereafter. Could you please give a good suggestion. > > Thanks in advance, > > Regards, > > S.Mahalakshmi > > > On Tue, Jul 6, 2010 at 6:46 PM, James W. MacDonald > <jmacdon at="" med.umich.edu="" <mailto:jmacdon="" at="" med.umich.edu="">> wrote: > > Hi S.Mahalakshmi, > > > On 7/6/2010 1:11 AM, mahalakshmi sivamani wrote: > > Hi, > > I have a set of genes and its chromosomal physical position in a > text file. > I want to view those genes in the chromosome using R package > GenePlotter. > Could any one please tell how to view this. > > > Have you looked at the vignettes for this package? What have you > tried so far? > > You will get much more traction if you show that you have at least > made an attempt to figure things out for yourself, and show where > things went wrong. > > Best, > > Jim > > > > Thanks in advance. > > > Yours sincerely, > > S.Mahalakshmi > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > <mailto: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 > > -- 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