[Bioc-devel] SummarizedExperiment

Tim Triche, Jr. tim.triche at gmail.com
Tue Mar 25 17:42:39 CET 2014

If it makes genosets coercible into SEs then I'm all for the change and its permanence


> On Mar 25, 2014, at 9:31 AM, Peter Haverty <haverty.peter at gene.com> wrote:
> One benefit of having dimnames on assays would be that one could use
> DataFrames as assays, like in eSet.  My genoset class is becoming more and
> more like SummarizedExperiment. The dimname issues prevent me from
> switching entirely from eSet to SummarizedExperiment.
> I think that keeping only one copy of dimnames is a great feature, if a bit
> dangerous.  My typical object has ~6 BigMatrix and/or DataFrame of Rle
> objects as assays, so the rownames actually make up a considerable portion
> of the object size.  (My typical dataset is 2.5M rows by 1k samples). I've
> been moving towards keeping a single dimnames copy just to improve RData
> load times.
> I think that assays should be required to have dimnames when they are added
> to a SummarizedExperiment. These dimnames should be checked for equality
> with the dimnames of the SE in the setter function.
> Perhaps with the recent (R 3.1) improvements in shallow/lazy copying and
> reference counting, adding dimnames to outgoing assays will be less of a
> performance hit.
> I also like the compromise I have seen elsewhere, where the colnames are
> always retained on assays, but only one rownames copy is kept.  Colnames
> are typically small and getting them wrong often makes for silent, but
> catastrophic errors.
> Pete
> ____________________
> Peter M. Haverty, Ph.D.
> Genentech, Inc.
> phaverty at gene.com
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