[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Kasper Daniel Hansen]

I see how an eSet maps to a SummarizedExperiment; one can look at the
assays in the object.  I agree with Levi/Herve that this is the natural
(correct) choice.  It is less clear how you get the ranges for a
RangedSummarizedExperiment without making assumptions.

On Mon, Sep 11, 2017 at 8:09 PM, Hervé Pagès <hpages at fredhutch.org> wrote:

> 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.bio
>> conductor.org_packages_devel_bioc_vignettes_Biobase_inst_
>> doc_BiobaseDevelopment.pdf&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfh
>> Q&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=s44znXbg9V
>> OxQh0qMe4z7PQsjrI_ZPrh4zdjiDO4rQg&s=C-oKupgUQZm6PA2e1IWSKKQq
>> PsQIy4uTGUg_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”
>>
>>
>>>
>>         [[alternative HTML version deleted]]
>>
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>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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