Hello, I am currently trying to annotate my Illumina microarray. I am not familiar with bioconductor and I am therefore relying on vignettes for help. I am trying to use lumiHumanAll.db to annotate my data but I can't get it to work. If I follow the examples in the pdf I can get a couple of genes printed out but I need to annotate the entire dataset. When I used GEO datasets with affy package I was able to get the annotation and then merge that with the GEO data and save a new file which contained both the GEO dataset and annotation. Is there a script that will do that for illumina data? I really need any help that anyone can give me. I am by no means a bioinformatician. Thanks for your help. Katie

Hi Katie, It is hard to help you based on the open ended nature of your question here. You might want to have a look at the posting guide here so that you can ask more specific questions: http://www.bioconductor.org/docs/postingGuide.html Also, if you are using the lumiHumanAll.db package, you probably want to look at the lumi package and it's vignettes for some further clarifications. http://www.bioconductor.org/packages/release/bioc/html/lumi.html Marc On 05/04/2010 03:00 AM, Katie wrote: > Hello, > > I am currently trying to annotate my Illumina microarray. I am not familiar > with bioconductor and I am therefore relying on vignettes for help. I am > trying to use lumiHumanAll.db to annotate my data but I can't get it to work. > If I follow the examples in the pdf I can get a couple of genes printed out > but I need to annotate the entire dataset. When I used GEO datasets with affy > package I was able to get the annotation and then merge that with the GEO data > and save a new file which contained both the GEO dataset and annotation. Is > there a script that will do that for illumina data? I really need any help > that anyone can give me. I am by no means a bioinformatician. > > Thanks for your help. > > Katie > > _______________________________________________ > 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 > >