[BioC] Problem loading affy using a saved workspace

[James MacDonald]

A little more information. The workspace I am loading contains two AffyBatch objects, and an exprSet object that was created by running rma on one of the AffyBatch objects.

If I load the workspace, delete the exprSet, and then load either Biobase or affy, things work as expected. It doesn't help to delete either of the AffyBatch objects.

Is there any reason that an existing exprSet object should be mucking things up?

Jim



James W. MacDonald
UMCCC Microarray Core Facility
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> Vincent Carey 525-2265 <stvjc at channing.harvard.edu> 03/27/03 03:34PM >>>
what version of R

exprSet undefined suggests package Biobase has not been loaded.
not clear to me why library(affy) does not accomplish the load.
try manually library(Biobase) before library(affy)

> Hi all,
>
> I am running R/Bioconductor on WinXP using affy 1.1.1. (Biobase 1.3.10)
>
> If I decide to open up an existing workspace that contains e.g., an AffyBatch and exprSet, I can open the workspace, but when I try to attach the affy package, I get the following error message.
>
> [Previously saved workspace restored]
>
> > library(affy)
> Loading required package: tkWidgets
> Loading required package: widgetTools

-----> this second load of tkWidgets is also strange -- i see it myself

> Loading required package: tkWidgets
>
> Attaching package `tkWidgets':
>
>
>         The following object(s) are masked from package:tkWidgets :
>
>          [snip]
>
> Error in mlistMetaName(f) : No way to associate a generic function with an object of class "NULL"
> Error in mlistMetaName(f) : No way to associate a generic function with an object of class "NULL"
> Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses) :
>         Class "AffyBatch" extends an undefined class ("exprSet"
> Error in library(affy) : .First.lib failed
> >
>
> Any ideas?
>
> Jim
>
>
>
>
> James W. MacDonald
> UMCCC Microarray Core Facility
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
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>