[BioC] Nimblegen arrays/Limma package:duplicate correlation and other problems

[Sean Davis]

On Tuesday 27 March 2007 11:13, Jenny Drnevich wrote:
> Hi Niki,
>
> I guess it's not exactly clear in the help page for lmFit, but
> correlation is only used if ndups > 1 or block is not NULL. Since you
> shouldn't be using either of these, correlation won't be used and
> hence the default value doesn't matter. This is all explained better
> in the vignette, under Technical Replication.

And just to be *absolutely* clear, you do not have replication on the 
array--is that correct?  It looked from the "genes" slot that there might be 
replication, but it wasn't possible to tell.  If not, is there a "tiling" 
component to the array, such as tiling of the promoter regions?

Sean