[BioC] limma, p values and missing data or weights 0

[Gordon K Smyth]

On Wed, 4 Jun 2008, sergiba at yahoo.com wrote:

> Dear Gordon and Limma users,
>
> I am using limma 2.12.0 (also tested 2.14.3) to analyze two-color arrays which
> have a common reference and I think I am not getting the expected output from
> lmFit() and eBayes().
>
> Data from these arrays is not very good and I used weights to flag spots which
> did not meet the quality criteria I had set.

> If I am not mistaken, in previous limma versions whenever you had only one
> measurement per row and the rest were "NA", no p.values were calculated (which
> makes sense to me). I believe the same happened if only one weight for a spot
> was 1 ( being the others equal to 0).

You are mistaken.  limma has always been able to give p.values, even when 
only a single observation is available, provided the contrast is 
estimable.  For these genes, the prior residual standard deviation is 
used.

Best wishes
Gordon