[Bioc-devel] SummarizedExperiment initialisation and manipulation question.

Nicolas Delhomme nicolas.delhomme at umu.se
Mon Jun 29 12:13:47 CEST 2015

Hej alla!

In the simpleRNASeq function of the easyRNASeq package, I start by instantiating a SummarizedExperiment object not initially providing the rowRanges. This results in the creation of an object of the class SummarizedExperiment0. When later, once I have validated the annotation, I try to extend the rowRanges of my SummarizedExperiment object, I get an error message that "rowRanges<-" is not implemented for signature "SummarizedExperiment0, GRangesList".

I'm now wondering if this has been omitted on purpose for SummarizedExperiment0 objects or is not yet implemented. The reason I'm wondering is because there is the possibility to cast a SummarizedExperiment0 object as a RangedSummarizedExperiment (which is my current work-around), but I'm wondering if that's the best way to go. 

I don't have access to my Rsession right now, so no sessionInfo(), but I'm using R3.2.1 on OSX 10.10.3 (Yosemite), and the latest devel packages (updated today; SummarizedExperiment version is 0.3.0).


Nicolas Delhomme, PhD

The Street Lab
Department of Plant Physiology
Umeå Plant Science Center

Tel: +46 90 786 5478
Email: nicolas.delhomme at umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden

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