[BioC] design and contrat matrix in limma for Affymetrix arrays

[James W. MacDonald]

Hi Jorge,

On 8/28/2012 10:34 AM, Jorge Miró wrote:
> 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:

Looks good to me.

Best,

Jim


>
> #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
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099