Hi,

I am trying to understand how to make the design matrix and the contrat
matrix for my analysis of gene expressions but I really can't figure it out.
What I have is 9 arrays where three of them correspond to untreated
individuals (groupA), another three correpond to a low level of treatment
(groupB) and the last three to a higher level of treatment (groupC). What I
want to do is to compare the  treatments and check what genes have been
affected in some kind of loop design, i.e groupA compared with
groupB, groupA compared with groupC and groupB compared with groupC.
I have read in the limma user guide and think a design matrix like the one
below could do what I want but I'm really not sure if I'm doing something
wrong:

#COntruct design matrix
> design <- model.matrix(~ 0+factor(c(1,1,1,2,2,2,3,3,3)))
> colnames(design) <- c('GroupA', 'GroupB', 'GroupC')

#Contruct contrast matrix
> contrast.matrix <- makeContrasts(GroupB-GroupA, GroupC-GroupA,
GroupC-GroupB, levels=design)

#Print design matrix
> design
  GroupA GroupB GroupC
1      1      0      0
2      1      0      0
3      1      0      0
4      0      1      0
5      0      1      0
6      0      1      0
7      0      0      1
8      0      0      1
9      0      0      1
attr(,"assign")
[1] 1 1 1
attr(,"contrasts")
attr(,"contrasts")$`factor(c(1, 1, 1, 2, 2, 2, 3, 3, 3))`
[1] "contr.treatment"

#Print contrast matrix
> contrast.matrix
        Contrasts
Levels   GroupB - GroupA GroupC - GroupA GroupC - GroupB
  GroupA              -1              -1               0
  GroupB               1               0              -1
  GroupC               0               1               1


#Session info
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252
 LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C
 LC_TIME=Swedish_Sweden.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] limma_3.12.1       Biobase_2.16.0     BiocGenerics_0.2.0

loaded via a namespace (and not attached):
[1] affylmGUI_1.30.0      IRanges_1.14.4        oneChannelGUI_1.22.10
stats4_2.15.0         tcltk_2.15.0
>

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