[R] LIMMA: array spot summary options beyond duplicateCorrelation()

From: Quin Wills <wills_at_stats.ox.ac.uk>
Date: Thu, 13 Mar 2008 20:35:08 +0000


Hello Limma users

A quick question, I hope:

I have dual-channel spotted expression arrays in a simple loop design (no dye swaps), viz:

1 vs reference
2 vs 1
3 vs 2
reference vs 3

There are 4 replicate spots for each probe on each array.

It seems as if getting meaningful spot summary results using duplicateCorrelation() is not possible in my case as the spots are not regularly spaced, and I don't *really* have enough arrays, no?

So then what are my other options in Limma to summarise replicated spots?

Thanks,
Quin

*Quin Wills*
*DPhil candidate*

*Department of Statistics*

*University** of Oxford***

*1 South Parks Road*
*Oxford***

*OX1 3TG

United Kingdom*  

*01865 285 394*

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