[BioC] Problems annotating a gene list

[Quentin Anstee]

Hi Jim,

Thanks. That does exactly what I was trying to achieve. The affycoretools
package promises to be a great addition to the BioC armoury.

All the best,

Quentin 

> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
> Sent: 24 February 2006 22:20
> Cc: Quentin Anstee; Bioconductor
> Subject: Re: [BioC] Problems annotating a gene list
> 
> Hi Quentin,
> 
> You might look at limma2annaffy() in the affycoretools 
> package. It will take your design matrix, contrast matrix, 
> exprSet, and MArrayLM objects and output HTML and/or text 
> tables with all the probesets annotated.
> 
> This package is in the devel repository, so you will not be 
> able to get it using e.g., biocLite() unless you are running 
> R-2.3.0dev. However, it doesn't require the devel version of 
> R, so you can download by hand and install using either the 
> dropdown menu (if you are using win32) or R CMD INSTALL if 
> you are on a Unix variant.
> 
> HTH,
> 
> Jim
> 
> 
> Sean Davis wrote:
> > 
> > 
> > On 2/24/06 12:58 PM, "Quentin Anstee" 
> <q.anstee at imperial.ac.uk> wrote:
> > 
> > 
> >>Hi Sean,
> >>
> >>Thanks for coming back to me on this one.
> >>
> >>I have had a look at 'fit2$genes', all it contains are the 
> affy probe 
> >>IDs as you predicted. Could you describe how to make the 
> annotations 
> >>and attach them to the MArrayLM file or let me know where 
> this process 
> >>is described? I have had a look in the limma help files and 
> vignette 
> >>but have not been able to find a walk through of this procedure.
> > 
> > 
> > It will suffice to make a data.frame in the same order and 
> containing 
> > the same number of genes at fit2$genes.  If your new data.frame is 
> > called gene.data, you just say fit2$genes <- gene.data.
> > 
> > You might want to look at the annaffy package and vignette for some 
> > ideas about how to ge the information you want from the 
> annotation package.
> > 
> > Sean
> > 
> > _______________________________________________
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> 
> 
> --
> James W. MacDonald
> University of Michigan
> Affymetrix and cDNA Microarray Core
> 1500 E Medical Center Drive
> Ann Arbor MI 48109
> 734-647-5623
> 
> 
> 
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