[BioC] Problem with "as.matrix.vsn" and "duplicateCorrelation" from limma

Wolfgang Huber huber at ebi.ac.uk
Sun Sep 16 02:07:38 CEST 2007


Dear Artur,

there is no "as.matrix" function for objects of type "vsn", such as 
returned by the "vsn2" function. You are right to use the "exprs" 
accessor instead.

If you are looking for a wrapper to vsn2 that produces an ExpressionSet 
(rather than a vsn object), please look at "justvsn" (in the devel 
branch, will be in the bioc 2.1 release).

Best wishes
	Wolfgang

> Hi all,
> 
> I just wanted to report an error that I've been geting:
> When I run duplicateCorrelation on this vsn object I get an error message.
> If instead of using the vsn object I use the result of an "expres(
> vsn.object)" function call it apparently works.
> I could be mistaken, but I don't think that I upgraded my packages or R and
> duplicateCorrelation after the last time I used duplicateCorrelation
> succesfully.
> 
> Thanks a lot!
> 
> Artur Veloso
> 
> Masters in Marine Biology Candidate
> College of Charleston, South Carolina, USA
> 
>> oyster.red.vsn <- vsn2(oyster.micro.red$G)
>> oyster.urbanization.correlation <- duplicateCorrelation(oyster.red.vsn,
> urbanization.design,ndups=2,spacing=1)
> Error in p(object) : no slot of name "assayData" for this object of class
> "vsn"
> 
> 
> # this function call works
>> oyster.site.creek.correlation <- duplicateCorrelation(exprs(oyster.red.vsn
> ),site.creek.design,ndups=2,spacing=1)
> 
> 
> 
>> sessionInfo()
> R version 2.5.1 (2007-06-27)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "methods"   "base"
> 
> other attached packages:
>  statmod      vsn     affy   affyio  Biobase    limma
>  "1.3.0"  "2.2.0" "1.14.2"  "1.4.1" " 1.14.1" "2.10.5"
> 
> 	[[alternative HTML version deleted]]
>



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