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 <hpa...@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]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et >> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt >> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=s4 >> 4znXbg9VOxQh0qMe4z7PQsjrI_ZPrh4zdjiDO4rQg&s=qKI2hqP0ltgK5_ >> LBtVFG6Va-8XAUuGwbXp9eKUfulXs&e= >> >> > -- > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
