[BioC] Limma: can't coerce Rgmodel into exprSet

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Fri Jun 4 14:39:58 CEST 2004

Hi James

Thanks for that!  This ties together with my posts yesterday - I want to
use the Biobase function esApply on my limma data, and esApply uses
exprSet objects.  Can I also coerce MA objects into exprSet objects
through this method?


-----Original Message-----
From: James Wettenhall [mailto:wettenhall at wehi.edu.au] 
Sent: 04 June 2004 13:14
To: michael watson (IAH-C)
Cc: bioconductor at stat.math.ethz.ch; Matthew Ritchie
Subject: Re: [BioC] Limma: can't coerce Rgmodel into exprSet

Hi Mick,

On Fri, 4 Jun 2004, michael watson (IAH-C) wrote:
> I have a kooperberg bg corrected dataset in limma and I want to coerce

> it to an exprSet object so that I can do some other stuff with it.  I
> > as(RGmodel, "exprSet")
> Error in as(RGmodel, "exprSet") : No method or default for coercing 
> "list" to "exprSet"

limma used to use regular lists for RG data but now it uses S4 
objects of class RGList.  Matt Ritchie wrote the kooperberg 
function, so I'm CCing the email to him.  He has (for the 
moment) used the old style (just a regular list).  You can 
convert it to the new style with:

RGobj <- new("RGList",.Data=RGmodel)

Hope this helps,

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