Thanks Sean! Your reply was very helpful. I already got almost what I wanted. I have some NA values but I will look if I can find them through bibliography or an external tool.
Best Regards, Eleni On Mon, May 19, 2008 at 6:07 PM, Sean Davis <[EMAIL PROTECTED]> wrote: > On Mon, May 19, 2008 at 10:47 AM, Eleni Christodoulou > <[EMAIL PROTECTED]> wrote: > > Dear list, > > > > I am having a set of human oligo ids (H200006022 H200002025 H300004703 > > H200000442 H200005719 H300018350) which I want to map to Ensembl or > RefSeq. > > I am sure R has a function to do that. I downloaded the {oligo} package > and > > tried to use the probeNames function. Although the factor of ologo ids is > an > > object (as the argument to probeNames should be) I retrieve the following > > error: > > probeNames(significant_genes[,1]) > > Error in function (classes, fdef, mtable) : > > unable to find an inherited method for function "probeNames", for > > signature "factor" > > > > where significant_genes is the factor with the oligo ids. Could anyone > help > > me with the format I should use in order to apply probeNames? Or if > someone > > has any other function in mind which can do the mapping I would be really > > grateful to hear that. > > Hi, Eleni. The probeNames() function is not applicable here, > unfortunately. You are asking a question related to annotating your > array. Therefore, you need an annotation package. I think the IDs > that you specified are Qiagen (Operon) IDs, so the place to look is in > the annotation package associated with the Qiagen arrays: > > Assuming that you are using R 2.7.0 (you are, correct?), then you can do: > > source('http://bioconductor.org/biocLite.R') > biocLite('hguqiagenv3.db') > library(hguqiagenv3.db) > mget(c('H200006022','H200002025'),hguqiagenenv3REFSEQ) > > The last command will return a list of mappings between those two > oligo ids and RefSeq. Typing: > > hguqiagenv3() > > will tell you the other annotation sources available for your qiagen > chip. Ensembl mappings are available, as are a bunch of other > mappings. > > Let us know if you have more questions. > > Sean > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.