[BioC] Limma and creating design matrices for complex loop designs
michael watson (IAH-C)
michael.watson at bbsrc.ac.uk
Fri Dec 9 12:21:49 CET 2005
I would like to respectfully request more examples of the creation of
design matrices for complex (ie involving more than 3 samples) loop
designs using two-colour microarrays in the limma documentation.
Although section 20.5 does give an example, with 5 RNA samples, one of
these is a pool which makes an obvious reference when creating the
design matrix as it is a coefficent we are not interested in estimating.
However, other loop designs may not contain such an obvious sample, and
I am struggling to figure out a way to create a design matrix for my
current design that allows all contrasts of interest. In fact, at
present, I have to create one design matrix to get some of the contrasts
and another to get the rest. Is this a valid approach?
More information about the Bioconductor