[BioC] averaging replicates within arrays

[Gordon K Smyth]

On Thu, November 10, 2005 3:03 am, alex lam \(RI\) wrote:
> I should rephrase the comment on the spots with zero weights. I knew that they were ignored in
> normalization. Are they also ignored in other limma methods? I had to explicitly exclude them in
> boxplot, but I guess boxplot is just a generic method.
>
> Regards,
> Alex
> ------------------------------------
> Alex Lam
> PhD student
> Department of Genetics and Genomics
> Roslin Institute (Edinburgh)
> Roslin
> Midlothian EH25 9PS
>
> Phone +44 131 5274471
> Web   http://www.roslin.ac.uk

All differential expression methods in limma take into account weights.  Basically
normalizeWithinArrays, lmFit, contrast.fit and plotMA() do.  Other functions which take results
from these functions inherit the treatment of weights.

Functions like boxplot() which are just R functions can't be expected to handle weights.

When in doubt, the help pages will tell you.  If a function has a 'weights' argument or similar,
then it uses weights.

Best wishes
Gordon