

Dear All,

Anyone can kindly provide me some insights/comments on how to analyze the data
using either LIMMA or other tools?

Thanks,
Qin
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Dear All,

say I have the following samples:

f1_A1
f1_A2
f1_B1
f1_B2
f2_C1
f2_C2
f2_D1
f2_D2

Here
f1 and f2 are two families
A1 and A2 are technical replicate. same for B1 and B2,C1 and C2, D1 and D2.
A,B,C,D are biological replicate, say A,C are affected while B,D are unaffected.
Noted some families have more than 1 affected or unaffected samples.

How does LIMMA take the two-level (technical replicate and familial relationship)
dependence into account?


Can I just simply do this way:

When I calculate duplicateCorrelation, I can set my block as
myblock<-c(1,1,2,2,3,3,4,4), #here take the technical replicate into account

When I do lmFit, I set the design and block as
s<- factor(c(1,1,0,0,1,1,0,0))  #1-affected and 0-unaffected
design <- model.matrix(~0+s)
myblock<-c(1,1,1,1,2,2,2,2)     #two-families

Here I used two different blocks in duplicateCorrelation and lmFit, looks not right....


Thanks,

Qin Kuang

 		 	   		  

 		 	   		  
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