[BioC] affy express->"No convergence... too many outliers"

[Carleton Garrett]

I am working through the example in the documentation 'Text Description
of affy' which creates an exprSet 'LiWong' using express() with the
'Dilution' dataset and summary.stat=li.wong).  I get the following
messages:

Normalizing Data
Background correcting
Preparing Data
Computing expression. This may take a while.
Warning messages:
1: No convergence achieved, too many outliers in:
fit.li.wong(t(data.matrix), remove.outliers, normal.array.quantile,
2: No convergence achieved in outlier loop
 in: fit.li.wong(t(data.matrix), remove.outliers, normal.array.quantile,

3: No convergence achieved, too many outliers in:
fit.li.wong(t(data.matrix), remove.outliers, normal.array.quantile,
4: No convergence achieved, too many outliers in:
fit.li.wong(t(data.matrix), remove.outliers, normal.array.quantile,

It doesn't seem to cause much of a problem with the Dilution dataset as
I can get the 'correct' results when I test the resulting exprSet with
the 'assess' function described in the document.

However, when I use a significantly bigger dataset (16 U133A chips) that
I have collected into a plob class, I get 50+ similar warnings about
outliers and the exprSet 'LiWong' is not created at the conclusion of
express().

Any thoughts regarding the origin of these warnings or how to avoid
them?

(I am working on a windows NT platform with R1.5.1 and all packages
obtained after June 26, 256 RAM, >70Gb harddrive)

Thanks

Carleton Garrett