[BioC] Limma normalization error and loess.R segmentation type fault (windows)

[Gordon K Smyth]

Hi Marcus,

I guess the fundamental question then is, what should loess normalization 
return (for a array or print-tip group or whatever) when all the weights 
are zero?

Strict mathematics would suggest that the solution should be NA.

Practical considerations suggest to me that normalizeWithinArrays() might 
be better performing ordinary unweighted loess normalization in this case, 
because no probe is weighted as more reliable than any other.

Or alternatively, one might say that the loess curve can't be estimated, 
so the raw expression values should be returned without adjustment.  So 
loess normalization with zero weights is equivalent to no normalization. 
That is what loessFit() and normalizeWithinArrays() have been doing up to 
R 2.14.1.

If you make the weights all zero for a print tip, do you want 
normalizeWithinArrays to return NAs for all probes in that print tip group 
on that array?  Or do ordinary unweighted normalization?  Or do no 
normalization?

Regards
Gordon

On Wed, 5 Sep 2012, Marcus Davy wrote:

> It looks like this error is related to a particular print tip having all
> weights=0 as input into stats:::simpleLoess. I am trying to construct a
> simple reproducible example.
>
> Marcus

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