Hi groups,

Suppose that the experiment has three cell-lines: c1, c2, c3
                                                     and three treatments: t1, t2, t3

The targets frame:

----------------------------------------------
filename     cell_line     treatment
----------------------------------------------
filename1    c1                t1
filename2    c2                t1
filename3    c3                t1
filename4    c1                t2
filename5    c2                t2
filename6    c3                t2
filename7    c1                t3
filename8    c2                t3
filename9    c3                t3
-----------------------------------------------


targets<-readTargets("targets.txt",sep=" ",row.names="fileneame")

What is the difference among:

1. design<-model.matrix(~-1+factor(targets$cell_line)+factor(targets$treatment))
2. design<-model.matrix(~-1+factor(targets$treatment)+factor(targets$cell_line))
3. design<-model.matrix(~factor(targets$cell_line)+factor(targets$treatment))
4. design<-model.matrix(~factor(targets$treatment)+factor(targets$cell_line))

and how could I make contrasts if I want to compare the difference among the treatments?

Thanks a lots.

Yours sincerely,

Jianhong Ou

jianhong.ou@umassmed.edu<mailto:jianhong.ou@umassmed.edu>



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