[BioC] help with design matrix

[maria kamarinos]

Dear All

I am working through the Apo1 example from the LIMMA users guide and
adapting it to my data but am having some trouble with the design
matrix and final data interpretation. I have the following
experimental set up with my goal being to identify which genes are
differentially expressed between test condition 1 and test condition
2.

array#76…..test1(Cy3) vs reference(cy5)
array#74…..test2(Cy3) vs reference(cy5)
array#80…..reference(Cy3) vs test1(cy5)
array#73…reference(Cy3) vs test2(Cy5)

I have read in my four GenePix files and gal file and normalized using
the print-tip lowess algorithm with no problems. I am using the
following targets file:

SlideNumber	        FileName	Cy3	Cy5
76	        slide76.gpr	test1	reference
74	        slide74.gpr	test2	reference
80	        slide80.gpr	reference	test1
73	        slide73.gpr	reference	test2

The following design matrix has been generated using the above targets
file and designMatrix()

               test1     test2
slide76     1      0
slide74     1     -1
slide80    -1      0
slide73    -1     -1

Is this design matrix appropriate if I am interested in comparing
test1 to test2?

If I was to use this design matrix (assuming I do not need a contrast
matrix) and perform empirical bayes statistical analysis on the data
to generate M values would negative M values that I get from toptable
(coef =2) indicate genes that are down regulated in test condition 2
and positive Ms those that are up regulated?
 
Thanks for your help

Maria Kamarinos