[BioC] How to create a design matrix for a three-way design?
january.weiner at mpiib-berlin.mpg.de
Fri Mar 26 09:03:11 CET 2010
I would be grateful for any kind of hint -- redirection to other
posts, documents, examples etc. I have trouble getting a clear picture
how I should create the design matrix and extract the contrasts.
I have the following situation: I am comparing two strains of cells,
wild type and mutant. The cells are subjected to treatment (T) or kept
as control (C), and RNA is collected at two different times after
experiment setup (t1, t2). What I would like to know is whether the
response to treatment is different in the wild type and the mutant at
any point in time. Two-color arrays are used with dye-swaps, and in
each the treatment is compared to the appropriate control.
My targets look like this:
What I did (and what was surely not correct) was to call any "C" as
"control", and use this as a reference:
design <- modelMatrix( target, ref="control" )
fit <- lmFit( ma, design )
contrast <- makeContrast( foo=(wt_t1-mu_t1)+(wt_t2-mu_t2), levels=design)
fit2 <- contrasts.fit( fit, contrast )
fit2 <- eBayes( fit )
etc. This seems to work... somewhat. If I run separate contrasts to
compare wt and mu at t1, and wt and mu at t2, I get different results,
and also way more significant. I am confused.
-------- Dr. January Weiner 3 --------------------------------------
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