[BioC] design a modelMatrix with no common references

[Giusy Della Gatta]

Hi everybody,

I have Agilent two colors expression arrays in which have been analyzed 
two KO mice samples (myc-/- and Rag -/-) treated with CD3 and with PBS.
I have a total of 4 arrays composed as follows:
     Sample   Cy3         Cy5
1. Myc24CD3	Myc_CD3	Myc_PBS (Swap)	
2. Myc24PBS	Myc_PBS	Myc_CD3	
3. Rag24CD3	Rag_CD3	Rag_PBS (Swap)		
4. Rag24PBS	Rag_PBS	Rag_CD3	

After the normalization I don't know
how to proceed for the  construction of the model matrix.

By using the suggestions of the  "Direct Two Color Designs" example (chapter 7.4 LIMMA guide)
I did:


> targets
                 FileName     Cy3     Cy5 Collection_time
1 3_Myc24CD3gr_Myc24PBSre Myc_CD3 Myc_PBS             24h
2 9_Myc24PBSgr_Myc24CD3re Myc_PBS Myc_CD3             24h
3 5_Rag24CD3gr_Rag24PBSre Rag_CD3 Rag_PBS             24h
4 4_Rag24PBSgr_Rag24CD3re Rag_PBS Rag_CD3             24h

> designmyc= modelMatrix(targets, ref="Myc_PBS")
Found unique target names:
 Myc_CD3 Myc_PBS Rag_CD3 Rag_PBS

> designmyc
     Myc_CD3 Rag_CD3 Rag_PBS
[1,]      -1       0       0
[2,]       1       0       0
[3,]       0      -1       1
[4,]       0       1      -1

> fit = lmFit(MA.Rq, designmyc)
Coefficients not estimable: Rag_PBS 
Warning message:
Partial NA coefficients for 45018 probe(s)


But at this point I calculated just the ratios of Myc_CD3/Myc_PBS
and Rag_Myc/Myc_PBS (I am not really interested in this last one!).
How can I specify in the model matrix design that I need two different references
to calculate the following logratios:  Myc_CD3/Myc_PBS, Rag_Myc/Rag_PBS?


Thank you in advance!
Giusy