[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Hervé Pagès]

I don't know the reasons behind this choice, I didn't implement
these methods. It would make sense to have these coercions defined
for the eSet,SummarizedExperiment and eSet,RangedSummarizedExperiment
signatures if they only access the eSet part of the object.
I'll look into this.

H.

On 09/11/2017 04:50 PM, Levi Waldron wrote:
> Thanks Ludwig and Kasper. This old presentation from Martin also helped me
> a lot:
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_packages_devel_bioc_vignettes_Biobase_inst_doc_BiobaseDevelopment.pdf&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=s44znXbg9VOxQh0qMe4z7PQsjrI_ZPrh4zdjiDO4rQg&s=C-oKupgUQZm6PA2e1IWSKKQqPsQIy4uTGUg_CSvBeq4&e=
>
> But I still wonder, why provide the coercion for ExpressionSet, if
> providing it for eSet would work not only for ExpressionSet but for
> everything else derived from eSet? The coercion function seems to work fine
> on the eSet-derived NChannelSet-class {the assays=as.list(assayData(from))
>   seems to work regardless of the storage mode}:
>
>> library(Biobase)> library(SummarizedExperiment)> example("NChannelSet-class", echo=FALSE)> class(obj)[1] "NChannelSet"
> attr(,"package")
> [1] "Biobase"> is(obj, "eSet")[1] TRUE
>
>> storageMode(obj)[1] "lockedEnvironment"
>
>> makeSummarizedExperimentFromExpressionSet(obj) class:
> RangedSummarizedExperiment dim: 10 3 metadata(3): experimentData annotation
> protocolData assays(2): G R rownames(10): 1 2 ... 9 10 rowData names(0):
> colnames(3): A B C colData names(3): ChannelRData ChannelGData ChannelRAndG
>
>> as(obj, "RangedSummarizedExperiment")
>
> Error in as(obj, "RangedSummarizedExperiment") :
>    no method or default for coercing “NChannelSet” to
> “RangedSummarizedExperiment”
>
>>
>
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>
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-- 
Hervé Pagès

Program in Computational Biology
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