[BioC] LIMMA Error Message:Error in new("AnnotatedDataFrame", data = phenotypicdata) : trying to generate an object from a virtual class ("AnnotatedDataFrame")

[Martin Morgan]

Hi Sally --

"Sally" <sagoldes at shaw.ca> writes:

> Hi,
>
> I am using the current version of LIMMA (January 25, 2009) and am
> having the following error message from this script below:
>
> Error Message: Error in new("AnnotatedDataFrame", data =
> phenotypicdata) : trying to generate an object from a virtual class
> ("AnnotatedDataFrame")
>
> Problematic Script (Note this script was originally run successfully
> under the version of LIMMA current during the winter/spring of 2008,
> but is not working now):
>
>> setClass("AnnotatedDataFrame")
> [1] "AnnotatedDataFrame"

You are defining a new class, and it is hiding the definition of the
AnnotatedDataFrame class defined in Biobase; this is not related to
limma, and would not have run under a version of R current in winter /
spring 2008. Probably what you are intending is

> library(Biobase)
> adf<-new("AnnotatedDataFrame",data=phenotypicdata)

Martin

>> adf<-new("AnnotatedDataFrame",data=phenotypicdata)
>
> Here is my phenotypicdata:
>
>       species time c0M1 c 0 c0M2 c 0 c0M3 c 0 c0M4 c 0 s0M1 s 0 s0M2 s
> 0 s0M3 s 0 c24M1 c 24 c24M2 c 24 c24M3 c 24 s24M1 s 24 s24M2 s 24
> s24M3 s 24 s24M4 s 24 c48M1 c 48 c48M2 c 48 c48M3 c 48 s48M1 s 48
> s48M2 s 48 s48M3 s 48 s48M4 s 48 c96M1 c 96 c96M2 c 96 c96M3 c 96
> s96M1 s 96 s96M2 s 96 s96M3 s 96 s96M4 s 96
>
> Thank-you
>
> Sally Goldes
>
>
>
>
>
> 	[[alternative HTML version deleted]]
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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PO Box 19024 Seattle, WA 98109

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