[Bioc-devel] SummarizedExperiments

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Fri Sep 14 19:54:34 CEST 2012

Thanks for all the additional methods.  I still miss
  seqlevels, seqlengths, genome


On Wed, Sep 12, 2012 at 3:33 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 09/12/2012 12:15 PM, Kasper Daniel Hansen wrote:

>> One thing I have in my package that I find indispensable is combine
>> and (my own) combineList.  The later for combining > 2 objects, which
>> has a lot of possibilities for speed up especially if (very common)
>> all the objects have the same rowData, as opposed to Reduce(combine,
>> LIST)..  Usecase: you need to add additional samples to your
>> SummarizedExperiment.
> I found it difficult in Biobase to write combine methods for eSet, where
> you're really requiring a lot from the user (about the phenoData /
> featureData structured in the same way) or going through contortions to make
> it the same in a reasonable-but-ad-hoc way (e.g., when two columns are
> factors with the same set of levels but encoded differently). Maybe the
> effort required is proportional to the utility of the function provided...
> I'll give it some more thought.

In the abstract case it is hard to imagine combining different
SummarizedExperiments.  My usecase is almost always "additional
samples from the same experiment", and for that situation it is a lot
easier to imagine combining it.  You still need to check that the
granges are similar (and if not, expand some of the assayData with
zeroes or NA's), since the new samples may have coverage in locations
not assayed earlier.  Clearly factors are hard to handle and I assume
there are other hard to handle cases.  Nevertheless, I find such a
function incredibly useful.

I think it is entirely ok to assume that the user knows what (s)he is doing.


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