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]]
>
