[BioC] self-self hybridization and limma

[Na, Ren]

hello,

If we have many samples to be compared in an microarray experiment,
for example,

	tissueType1	tissueType2	tissueType3
age1	4		4		4
age2	4		4		4
age3	4		4		4
each kind of sample has 4 biological replicates, primary interest are differential 
expression among different age groups and among different tissueTypes. We usually 
use common reference design. I am wondering if I can use self-self hybridization design,
in which two identical samples are labeled with different dyes and hybridized to the 
same slide. maybe I don't need to worry about dye bias by using log-intensity A-value
for each spot, and use limma analyze like,
MA<-normalizeWithinArrays(RG, method="none")
MA<-normalizeBetweenArrays(MA, method="Aq")
convert MA to exprSet, then replace M-value in exprSet with A-value, then use the new 
exprSet to get significant genes using limma. I only know self-self experiment to be 
used to show imbalance in red and green intensity, but I never found it to be used to 
do real experiment. I think there must be some reasons that self-self hybridization is 
not appropriate. 
Could anyone explain it, Thanks in advance!

Ren

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