[BioC] Limma; matrix of microarray data and design matrix

[James W. MacDonald]

Hi John,

On 6/3/2011 9:20 AM, john herbert wrote:
> Dear Bioconductors.
> I have a six column matrix of one colour array data (first 3 columns are
> case, second 3 are control), quantile normalized.
>
> I would like to do simple differential gene expression using limma.
>
> Is there a line or two of code that generates a simple design matrix for
> this scenario?
>
> I usually use a design matrix created from a targets file, and I never
> really understand lines like...  design<- model.matrix(~0+f) (what is
> ~0+f)?

No idea what f is here (other than the obvious; it is a variable 
pointing to a set of factors).

But constructing the design matrix is simple.

f <- factor(rep(c("case","control"), each = 3)) # ;-D
design <- model.matrix(~f)
fit <- lmFit(<yourmatrix>, design)
fit2 <- eBayes(fit)
topTable(fit2, coef=2)

-OR-

design <- model.matrix(~0+f)
fit <- lmFit(<yourmatrix>, design)
fit2 <- contrasts.fit(fit, c(-1,1))
fit2 <- eBayes(fit2)
topTable(fit2, coef=1)

These results will be identical, except the signs will be flipped for 
your coefficients (and I would normally prefer the sign in the second 
case). It is worth your while to figure out why, and what the difference 
is between the two design matrices.

Best,

Jim


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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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