[BioC] Normalization in davidTiling demo

[Wolfgang Huber]

Dear Julian,

oh well. The non-linear optimisation routine L-BFGS-B that is used in 
vsn (which is used in normalizeByReference for between-array 
normalisation) can sometimes be a fit fiddly with its convergence 
criteria. It seems there are some OS- or compiler-specific differences.

I am currently working on a completely revised version of vsn, and once 
the normalizeByReference function has been been updated, this problem 
may be solved.

For the short term:

- use Linux, or

- note that vsn is only used for the between-array normalization; the 
main point of the normalizeByReference function is to adjust for probe 
effects. Hence you can call the function on each RNA-array separately, 
this will avoid the between-array normalization step but still do the 
same kind probe effect adjustment. You can then do the between-array 
normalization by some other means (e.g. just shift to the same median).

  Best wishes
    Wolfgang

> Hi Wolfgang,
> 
> I upgraded to tilingArray 1.13.3 and R-2.5 and I also
> upgraded all the other packages as far as I could, but I'm
> afraid with no effect.
> The problem doesn't occur on Linux, everything works fine
> there.
> Thanks for your quick response and help.
> 
> Greetings
> Julian Gehring