[BioC] Combining expressionSets from GEO

[Francois Pepin]

> combine does know how to deal with factors properly -- the levels are
> different, so the columns (usually) can't be combined. But I
> appreciate the sentiment, and the issue has come up on the mailing
> list three times since 2.1, so is a common occurrence. I've tried some
> more at making the documentation better, and will work on a better set
> of warnings for the next release of Bioconductor.

I understand why it wouldn't really work in the general case of
combining data.frames. But I do think that columns can be combined in
this specific case, especially considering the requirement that the
sample names be different. The ordering of the levels would have to be
somewhat arbitrary though, so I do not know if a warning would be
warranted in this case. It just seems strange that a perfectly legal
eSet cannot use one of the basic functionality described in that class.

> Actually, 'eSet' is a class that 'ExpressionSet' extends; 'eSet' is
> not going to away, and many of the data slots and methods on
> ExpressionSet are inherited from eSet so it's appropriate to
> reference the eSet documentation for these. The 'exprSet' class is no
> longer supported.

Yes, of course. I keep on mixing them.

Francois