[BioC] basic limma questions

[Endre Sebestyen]

Dear Gordon,

Thanks for the answers. I have one final question. It is true that the
Data-Ctrl contrast is the same in both cases, but it makes a
difference if my gene is 10x up or 0.1x downregulated compared to the
untreated sample. So either I have to change  R and G, or use a
design <- c(-1,-1,-1). Am I right?

Endre


On Tue, Apr 1, 2008 at 2:19 AM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
> Dear Endre,
>
>  It sounds as if limma recognised the ArrayVision format fine.  As far as I
>  know, there is no way to tell from the ArrayVision file which channel is
>  cy3 and which is cy5.  Even though limma got them the wrong way around in
>  this case, it doesn't really matter because it makes no difference to the
>  analysis.  The Data-Ctrl contrast is the same regardless of which is R and
>  which is G.
>
>  Best wishes
>  Gordon