[BioC] modelMatrix question

[Jason Skelton]

Hi
I have a question regarding the modelMatrix function in limma. 
Which has been covered before however I haven't found an appropriate answer in the 
documentation or the list archives.

Can one use modelMatrix to adjust for unequal numbers of technical 
replicates? To take a very simplified example for:

targetsx
	Cy3	Cy5
1	WT_sample1	Mutant_sample1
2	Mutant_sample1	WT_sample1
3	WT_sample2	Mutant_sample2
4	Mutant_sample3	WT_sample3

The samples being different biological replicates of single mutant and 
wild-type cell lines. So we would just want to average them together, but 
without biassing towards sample1 relatively to samples 2 and 3.

I thought I might be able to enter parameters like

parameters
		Mutant-WT
WT_sample1	-1/3
WT_sample2	-1/3
WT_sample3	-1/3
Mutant_sample1	1/3
Mutant_sample2	1/3
Mutant_sample3	1/3

to give the different replicates equal weight.
But this just gives me


>> modelMatrix(targetsx, parameters)
>  
>
Found unique target names:
 Mutant_sample1 Mutant_sample2 Mutant_sample3 WT_sample1 WT_sample2 
WT_sample3
  [,1]
1    1
2   -1
3    1
4   -1

which doesn't appear to be what I want
any help greatfully recieved

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