[Bioc-devel] SummarizedExperiment with alternate back end

[Hervé Pagès]

Hi Vince,

This is actually on "our" TODO list for after the release.
SummarizedExperiment was designed to support alternate back end
for the assays slot. More details and proof of concept are
in ?Assays.

H.

On 09/18/2015 01:29 PM, Vincent Carey wrote:
> i am dealing with ~700 450k arrays
>
> they are derived from one study, so it makes sense to think of
>
> them holistically.
>
> both the load time and the memory consumption are not satisfactory.
>
> has anyone worked on an object type that implements the rangedSE API but has
>
> the assay data out of memory?
>
>> unix.time(load("wbmse.rda"))
>
>     user  system elapsed
>
>   30.131   2.396  61.036
>
>> object.size(wbmse)
>
> 124031032 bytes
>
>> dim(wbmse)
>
> [1] 485577    690
>
>> object.size(assays(wbmse))
>
> 2680430992 bytes
>
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>
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-- 
Hervé Pagès

Program in Computational Biology
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