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On Mon, May 19, 2008 at 10:47 AM, Eleni Christodoulou <elenichri at="" gmail.com=""> 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