[BioC] problem with expresso()

[Wolfgang Huber]

Hi Laurent:

> Here is a suggestion:
> 1) "intermediate" processing steps must return data on the same
> scale than they received them
> 2) add two paramaters to functions like "normalize", "computeExpr":
> 'transfo' (and 'untransfo') to specify a transformation to apply before
> Would this appear satisfactory/reasonable ?

The combinatorics of all those different method could become quite
overwhelming. And that means also: potentially prone to bugs or user
mistakes, and inefficient (computation time, memory). To be able to combine
the different methods freely is extremely useful for people working on
method comparisons, but is this really the main goal of the affy package?

I still do not fully understand why there are both express() and expresso()
methods, and in addition there is now also a standalone implementation of
RMA in C. But could it be that this reflects the limitations of the
combinatorial approach?

Another approach that I'd suggest is to expect people that want to plug
together all sorts of different background adjustment, normalization,
transformation and probeset-summary methods to do so on their own
responsibility.

And for everyone else, you (we) can offer a small number of functions like
rma(), express(o) with limited options, that we have found to make sense.

What do you think?

Best regards
Wolfgang