[BioC] design a modelMatrix with no common references
Giusy Della Gatta
gd2253 at columbia.edu
Fri Jul 10 01:59:01 CEST 2009
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)
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
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
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!
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