


Dear Helper


For the Estrogen data given in limma usersguide, we can estimate estrogen effect and 
the time-estrogen interaction as follows

>  design=matrix(c(1,1,1,1,1,1,1,1,
+ 0,0,0,0,1,1,1,1,
+ 0,0,1,1,0,0,0,0,
+ 0,0,0,0,0,0,1,1),nrow=8,ncol=4, byrow=F)
> rownames(design)= treatments
> colnames(design)= c("Intercept","Time","E10","E48")
> 
> design
    Intercept Time E10 E48
e10         1    0   0   0
e10         1    0   0   0
E10         1    0   1   0
E10         1    0   1   0
e48         1    1   0   0
e48         1    1   0   0
E48         1    1   0   1
E48         1    1   0   1
> cont.matrix <- cbind(E10=c(0,0,1,0),E48=c(0,0,0,1),"E48-E10"=c(0,0,1,-1) )
> cont.matrix
     E10 E48 E48-E10
[1,]   0   0       0
[2,]   0   0       0
[3,]   1   0       1
[4,]   0   1      -1

The first and second coefficients (in cont.matrix) estimate the estrogen effect 
at 10 hours and 48 hours ,respectively. The third coefficient (in cont.matrix) 
estimates the time-estrogen interaction.

Here I want to ask another question:

Which genes have estrogen effect (up/down between absent and present) 
CONSISTENTLY at both 10 hours and 48 hours?

I am not sure how to add one item in either design or contrast matrix to do
this job ???

Is it an efficient way to just simply look the intersection of genes selected in 
first and second coefficients (in cont.matrix)?

Thank you very much for your help in advance !!!

Qin Kuang











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