[BioC] problem with duplicateCorrelation and ExpressionSet objects

[Seth Falcon]

Jenny Drnevich <drnevich at uiuc.edu> writes:

> Hi Gordon,
>
> I'm still having the problem with duplicateCorrelation on an 
> ExpressionSet object, even though I upgraded to limma 2.10.4. 
> Additionally, the 'fix' of not having the Matrix package loaded 
> doesn't work either, unless there's a difference between never having 
> loaded the package and detaching the package... Am I doing something
> wrong?

There is a difference between having a fresh R session in which a
package has never been loaded and an R session in which you have
detached a package.

Unfortunately, package loading/attaching is not a completely
reversible operation in all cases (some of the limitations are even at
the OS level when shared libraries are involved).

You can use loadedNamespaces() to see what namespaces are loaded and I
suspect that Matrix remains loaded even after you have detached it.
Why?  Well, because you have Category attached which Depends on
Matrix.

I think this is worth further investigation, because it seems to me
that the changes Gordon made should have solved this problem with or
without Matrix being loaded.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org