[Bioc-devel] renameModelMatrixColumns mishap + patch for DESeq2

[Steve Lianoglou]

Hi Kasper,

On Tue, Jul 9, 2013 at 5:51 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> This is side-stepping the question, but I am not aware that it ever makes
> sense to include the "A:B" term in a design matrix without also including
> the main effects of A and B (here I include obvious extensions such as A +
> A:B + C where B is a coarser factor than C, so here the main effects of B
> are essentially included).  Of course, the A+A:B+C example seems to also
> fail in the DESeq2 code you quote, but these examples are rare in comp bio.
>
> If you're just fitting a model like
>   A + A:B
> you're almost certainly doing something wrong from a statistical point of
> view.

Thanks for the input/guidance -- I'm always happy to get some
linear-modeling-schooling.

If that's the case, does that mean that I'm interpreting the advice
from the limma user's guide incorrectly? Page 44 in the "Nested
Interaction Formula" section:

http://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf

Aren't the coefficients extracted for cellA:treatment1,
cellA:treatment2, ..., cellD:treatment4 that you get when modeling
this way exactly the fold changes for the effect of the treatment
within each cell type?

Thanks,
-steve

--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech