[Bioc-devel] renameModelMatrixColumns mishap + patch for DESeq2

Steve Lianoglou lianoglou.steve at gene.com
Wed Jul 10 03:01:56 CEST 2013

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

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:


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?


Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology

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