I can load the annotation package. The problem I’m running into is with the beadarray package. When I use readIllumina() or try and set the annotation package, it says that it can only use Humanv1, etc. In this situation the methylation package I need isn’t supported, and I need to use it so I can analyze the data. I don’t have the exact information or code because the computer with R is doing a marathon 20 hour data processing thing and can’t handle running R at the same time, but I hope this is more clear than my last message. Alice Arcury-Quandt Research Assistant Department of Epidemiology Division of Public Health Sciences Wake Forest University School of Medicine Winston-Salem, NC 27157 From: seandavi@gmail.com [mailto:seandavi@gmail.com] On Behalf Of Sean Davis Sent: Friday, July 30, 2010 7:48 AM To: Alice E. Arcury-Quandt Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] beadarray methylation annotation question On Thu, Jul 29, 2010 at 1:19 PM, Alice E. Arcury-Quandt <aarcuryq@wfubmc.edu> wrote: Hi all, I'm working with an Illumina methylation dataset. I have the bead level data and can load it without any problem, but the annotation package I need to use (IlluminaHumanMethylation27k) isn't supported. Does anyone know how I can get around that? Hi, Alice. You'll want to be more specific about what the problem is, as IlluminaHumanMethylation27k.db is available in the current (and prior) bioconductor release. Also, as the posting guide suggests, it is bet to provide the output of sessionInfo() and perhaps code showing the problem you are having. My guess is that you need to upgrade to the latest R, but it is only a guess.... Sean [[alternative HTML version deleted]]