[BioC] [Fwd: help in annotation ILLUMINA probes]

[Steve Lianoglou]

Hi Dave,

On Wed, May 25, 2011 at 11:10 PM, Dave Tang <davetingpongtang at gmail.com> wrote:
> On Tue, 17 May 2011 17:12:13 +0900, Mark Dunning <mark.dunning at gmail.com>
> wrote:
>
>> Hi Nathalie,
>>
>> You can use the illumina Bioconductor annotation packages to do this.
>> The particular one you need is illuminaMousev2.db
>>
>>> library(illuminaMousev2.db)
>>
>>> ids = c("ILMN_1250814", "ILMN_1257855", "ILMN_2537948", "ILMN_3144164",
>>> "ILMN_2636200")
>>
>>> mget(ids, illuminaMousev2GENOMICLOCATION)
>
> Dear Mark,
>
> I ran the code but came across some problems. Here's my history
>
> library("AnnotationDbi")
> source("http://bioconductor.org/biocLite.R")
> biocLite("illuminaMousev2.db")
> library(illuminaMousev2.db)
> ids = c("ILMN_1250814", "ILMN_1257855", "ILMN_2537948", "ILMN_3144164",
> "ILMN_2636200")
> mget(ids, illuminaMousev2GENOMICLOCATION)
>
> Error: object 'illuminaMousev2GENOMICLOCATION' not found
> Error in mget(ids, illuminaMousev2GENOMICLOCATION) :
>  error in evaluating the argument 'envir' in selecting a method for function
> 'mget'
>
> sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-unknown-linux-gnu

As a general rule of thumb, you should be running the latest version
of the R and bioconductor combo to get the most milage out of the help
on this mailing list.

The latest version of R is 2.13.0, which was recently released. If you
use that with the appropriate bioconductor version (v 2.8 -- which is
chosen automatically for you when installing via biocLite()) the code
works as advertised.

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact