Hi All,

I have samples like this:
Targets.txt>>
Filename group replicates
V1            vec     rep1
V2            vec     rep2
V3            vec     rep3
A1            aec     rep1
A2            aec     rep2
A2            aec     rep2
C1             cec     rep1
C2             cec     rep2
C3             cec     rep3
D1             dec     rep1
D2             dec     rep2
D3             dec     rep3
E1             eec     rep1
E2             eec     rep2
E3             eec     rep3

If I want to compare group vec to all the others, is this correct I create model matrix and make contrasts like this,
design <- model.matrix(~-1+group)
colnames(design) <- gsub("^group","",colnames(design))
contrast.matrix <- makeContrasts(contrasts="vec-(aec+cec+dec+eec)/4", levels=design)

Or should I do it like,
block <- factor(c(rep("b1", 3), rep("b2",12)))
design <- model.matrix(~-1+block+block:group)
colnames(design) <- gsub("^block","",colnames(design))
contrast.matrix <- makeContrasts(contrasts="b1-b2", levels=design)

Thanks in advance for you help.

Yours sincerely,

Jianhong Ou

LRB 710
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605

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