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

 


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