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

[Jenny Drnevich]

To add to Sean's keen observation...

Are these expression arrays or tiling arrays? I've never worked with 
Nimblegen arrays, but ~390,000 spots seems like a lot for expression 
arrays. Also, you said this is chIP-on-chip data, right? If they are 
expression arrays with multiple spots, then you will need to use 
duplicateCorrelation to estimate the spot-replicate correlations. If 
they are tiling arrays (usually used with chIP-on-chip data), you 
will need to analyze it a completely different way because probes 
that are close to each other on the chromosome will not have 
independent fluorescence values.

Jenny

At 11:00 AM 3/27/2007, Sean Davis wrote:
>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

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

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