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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--
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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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