[BioC] Combining expressionSets from GEO

Martin Morgan mtmorgan at fhcrc.org
Thu Jan 31 00:21:11 CET 2008

Thanks to both for your feedback. I'm not sure whether the current
state represents an over-reaction to an earlier problem, or a more
reasoned position. I'll look through my notes and, if appropriate,
make the change to the way combine works. This will be in the
development version of Biobase, and will not be implemented for a
couple of weeks.

In some ways the current behavior of data.frame (automatically making
factors out of character strings) is the root of the problem, and to
me argues against being too clever in trying to guess the user's


Francois Pepin <fpepin at cs.mcgill.ca> writes:

>> 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

Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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