Dear list,

I have two design matrixes:

design<-model.matrix(~-1+factor(grp))
designcontr<-model.matrix(~factor(grp))

then make contrast matrix:
cont.matrix<-rbind(rep(-1,9),diag(9))
cont.matrix_contr <- rbind(rep(0,9),diag(9))

after using topTable to get the specific probe values, I found:
e.g.
using designcontr and cont.matrix_contr:
ID Coef1 Coef2 Coef3 Coef4 Coef5 Coef6 Coef7 Coef8 Coef9 AveExpr F P.Value 
adj.P.Val 

feature1 -0.07976 2.900216 3.06401 3.210565 0.229553 1.545972 2.433364 2.62326 
2.719911 13.18788 1133.135 1.60E-15 7.20E-11 


using design and cont.matrix:
ID Coef1 Coef2 Coef3 Coef4 Coef5 Coef6 Coef7 Coef8 Coef9 AveExpr F P.Value 
adj.P.Val 

feature1 -0.07976 0.229553 1.545972 2.433364 2.62326 2.719911 2.900216 3.06401 
3.210565 13.18788 1133.135 1.60E-15 7.20E-11 



I try to understand why there is difference between cont.matrix_contr and 
cont.matrx results, since both of them is try to get the difference between each 
grp(grp2 to grp10) and grp1. i.e. grp[i](i=2-10) - grp[1]

even I used the different contrasts, the coef should  be the same. I am 
confused. 


Thank you for your help.

Regards,
Xiaokuan


      
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