[BioC] LIMMA: Unbalanced technical replicates

[Ron Ophir]

Hi,
I have an affymetrix experiment with the following target file:
Replicates	FileName	Target
8	SA100Hu133plus.CEL	LR
4	SA101Hu133plus.CEL	LR
4	SA102Hu133plus.CEL	LR
4	SA103Hu133plus.CEL	LR
9	SA104Hu133plus.CEL	LR
5	SA105Hu133plus.CEL	LR
5	SA106Hu133plus.CEL	LR
10	SA107Hu133plus.CEL	LR
11	SA108Hu133plus.CEL	LR
12	SA109Hu133plus.CEL	MET
13	SA111Hu133plus.CEL	MET
14	SA112Hu133plus.CEL	MET
15	SA113Hu133plus.CEL	MET
16	SA114Hu133plus.CEL	MET
17	SA115Hu133plus.CEL	MET
18	SA116Hu133plus.CEL	MET
6	SA117Hu133plus.CEL	MET
6	SA119Hu133plus.CEL	MET
19	SA121Hu133plus.CEL	METD
20	SA122Hu133plus.CEL	METD
7	SA123Hu133plus.CEL	METD
7	SA124Hu133plus.CEL	METD
21	SA127Hu133plus.CEL	HR
1	SA83Hu133plus.CEL	HR
1	SA84Hu133plus.CEL	HR
1	SA85Hu133plus.CEL	HR
22	SA86Hu133plus.CEL	HR
2	SA87Hu133plus.CEL	HR
2	SA88Hu133plus.CEL	HR
2	SA89Hu133plus.CEL	HR
23	SA90Hu133plus.CEL	HR
3	SA92Hu133plus.CEL	HR
3	SA93Hu133plus.CEL	HR
24	SA94Hu133plus.CEL	HR
25	SA95Hu133plus.CEL	HR
26	SA96Hu133plus.CEL	HR
27	SA98Hu133plus.CEL	LR
28	SA99Hu133plus.CEL	LR
where files with the same number under replicates column are blocks of
the technical replicates of the sames biological replicate. 
and the following design:
	LR	HR	MET	METD
SA100Hu133plus.CEL	1	0	0	0
SA101Hu133plus.CEL	1	0	0	0
SA102Hu133plus.CEL	1	0	0	0
SA103Hu133plus.CEL	1	0	0	0
SA104Hu133plus.CEL	1	0	0	0
SA105Hu133plus.CEL	1	0	0	0
SA106Hu133plus.CEL	1	0	0	0
SA107Hu133plus.CEL	1	0	0	0
SA108Hu133plus.CEL	1	0	0	0
SA109Hu133plus.CEL	0	0	1	0
SA111Hu133plus.CEL	0	0	1	0
SA112Hu133plus.CEL	0	0	1	0
SA113Hu133plus.CEL	0	0	1	0
SA114Hu133plus.CEL	0	0	1	0
SA115Hu133plus.CEL	0	0	1	0
SA116Hu133plus.CEL	0	0	1	0
SA117Hu133plus.CEL	0	0	1	0
SA119Hu133plus.CEL	0	0	1	0
SA121Hu133plus.CEL	0	0	0	1
SA122Hu133plus.CEL	0	0	0	1
SA123Hu133plus.CEL	0	0	0	1
SA124Hu133plus.CEL	0	0	0	1
SA127Hu133plus.CEL	0	1	0	0
SA83Hu133plus.CEL	0	1	0	0
SA84Hu133plus.CEL	0	1	0	0
SA85Hu133plus.CEL	0	1	0	0
SA86Hu133plus.CEL	0	1	0	0
SA87Hu133plus.CEL	0	1	0	0
SA88Hu133plus.CEL	0	1	0	0
SA89Hu133plus.CEL	0	1	0	0
SA90Hu133plus.CEL	0	1	0	0
SA92Hu133plus.CEL	0	1	0	0
SA93Hu133plus.CEL	0	1	0	0
SA94Hu133plus.CEL	0	1	0	0
SA95Hu133plus.CEL	0	1	0	0
SA96Hu133plus.CEL	0	1	0	0
SA98Hu133plus.CEL	1	0	0	0
SA99Hu133plus.CEL	1	0	0	0
My question is should I run duplicateCorrelation function with this
vector 
B<-c( 8,  4,  4,  4,  9,  5,  5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 
6,  6, 19, 20,  7,  7, 21,  1,  11, 22,  2,  2,  2, 23,  3,  3, 24, 25,
26, 27, 28)
where each biological replicate gets different block number
or
B<-c(   4,  4,  4,   5,  5,  6,  6,   7,  7,   2,  2,  2, 3,  3, )
where I ignore biological replicates or maybe put zero instead of
biological replicates.

corfit <- duplicateCorrelation(data, design, block=B)

Thanks
Ron