Hi Michael
where would you put the “colData”-style metadata for the 3rd, 4th, … dimensions?
As an (ex-)physicists of course I like arrays, and the more dimensions the
better, but in practical work I’ve consistently been bitten by the rigidity of
such a design choice too early in a process.
Wolfgang
> On 31 Mar 2015, at 13:32, Michael Lawrence <lawrence.mich...@gene.com> wrote:
>
> Taken in the abstract, the tidy data argument is one for consistent data
> structures that enable interoperability, which is what we have with
> SummarizedExperiment. The "long form" or "tidy" data frame is an effective
> general representation, but if there is additional structure in your data,
> why not represent it formally? Given the way R lays out the data in arrays,
> it should be possible to add that fourth dimension, in an assay array, while
> still using the colData to annotate that structure. It does not make the data
> any less "tidy", but it does make it more structured.
>
> On Tue, Mar 31, 2015 at 4:14 AM, Wolfgang Huber <whu...@embl.de
> <mailto:whu...@embl.de>> wrote:
> Dear Jesper
>
> this is maybe not the answer you want to hear, but stuffing in 4, 5, …
> dimensions may not be all that useful, as you can always roll out these
> higher dimensions into the existing third (or even into the second, the
> SummarizedExperiment columns). There is Hadley’s concept of “tidy data” (see
> e.g. http://www.jstatsoft.org/v59/i10 <http://www.jstatsoft.org/v59/i10> ) —
> a paper that is really worthwhile to read — which implies that the tidy way
> forward is to stay with 2 (or maybe 3) dimensions in SummarizedExperiment,
> and to record the information that you’d otherwise stuff into the higher
> dimensions in the colData covariates.
>
> Wolfgang
>
> Wolfgang Huber
> Principal Investigator, EMBL Senior Scientist
> Genome Biology Unit
> European Molecular Biology Laboratory (EMBL)
> Heidelberg, Germany
>
> T +49-6221-3878823 <tel:%2B49-6221-3878823>
> wolfgang.hu...@embl.de <mailto:wolfgang.hu...@embl.de>
> http://www.huber.embl.de <http://www.huber.embl.de/>
>
>
>
>
>
> > On 30 Mar 2015, at 12:38, Jesper Gådin <jesper.ga...@gmail.com
> > <mailto:jesper.ga...@gmail.com>> wrote:
> >
> > Hi!
> >
> > The SummarizedExperiment class is an extremely powerful container for
> > biological data(thank you!), and all my thinking nowadays is just circling
> > around how to stuff it as effectively as possible.
> >
> > Have been using 3 dimension for a long time, which has been very
> > successful. Now I also have a case for using 4 dimensions. Everything
> > seemed to work as expected until I tried to subset my object, see example.
> >
> > library(GenomicRanges)
> >
> > rowRanges <- GRanges(
> > seqnames="chrx",
> > ranges=IRanges(start=1:3,end=4:6),
> > strand="*"
> > )
> >
> > coldata <- DataFrame(row.names=paste("s",1:3, sep=""))
> >
> > assays <- SimpleList()
> >
> > #two dim
> > assays[["dim2"]] <- array(0,dim=c(3,3))
> > se <- SummarizedExperiment(assays, rowRanges = rowRanges, colData=coldata)
> > se[1]
> > #works
> >
> > #three dim
> > assays[["dim3"]] <- array(0,dim=c(3,3,3))
> > se <- SummarizedExperiment(assays, rowRanges = rowRanges, colData=coldata)
> > se[1]
> > #works
> >
> > #four dim
> > assays[["dim4"]] <- array(0,dim=c(3,3,3,3))
> > se <- SummarizedExperiment(assays, rowRanges = rowRanges, colData=coldata)
> > se[1]
> > #does not work
> > #Error in x[i, , , drop = FALSE] : incorrect number of dimensions
> >
> > This is also the case for rbind and cbind. Would it be appropriate to ask
> > you to update the SE functions to handle subset, rbind, cbind also for 4
> > dimensions? I know the time for next release is very soon, so maybe it is
> > better to wait until after April 16. Just let me know your thoughts about
> > it.
> >
> > Jesper
> >
> > [[alternative HTML version deleted]]
> >
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