[BioC] duplicateCorrelation

[Jason Skelton]

Hi All

running duplicateCorrelation in limma

cor <- duplicateCorrelation(nwaMA, ndups=2, spacing=840, design)

I have three arrays with the following design
                  a  b  c
Array 1     1  0  0
Array 2     0 -1  0
Array 3     0  0 -1

The layout is:
$ngrid.r
[1] 12
 $ngrid.c
[1] 4
 $nspot.r
[1] 21
 $nspot.c
[1] 20

the correlation returned is 1 for every gene on the array ?
the M & A values for any given set of duplicates across the array are 
similar
and the original gpr files don't hint at anything obvious.

Subsequent analysis with lmFit will work but ebayes won't, which makes 
sense ?
as there are no degrees of freedom

If anyone has any suggestions

using R 1.9.1
using limma 1.8.1

many thanks
Jason

-- 
--------------------------------
Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919