[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Levi Waldron]

Thanks Ludwig and Kasper. This old presentation from Martin also helped me
a lot:

https://www.bioconductor.org/packages/devel/bioc/vignettes/Biobase/inst/doc/BiobaseDevelopment.pdf

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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