Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

One more thing. See below... On 09/13/2017 02:54 PM, Ludwig Geistlinger wrote: Coercing vice versa, i.e. from SummarizedExperiment to ExpressionSet, which is defined in SummarizedExperiment/R/makeSummarizedExperimentFromExpressionSet.R as follows: setAs("SummarizedExperiment",

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

Hi Ludwig, Excellent catch! Thanks for the report. This should be fixed in SummarizedExperiment release (1.6.4) and devel (1.7.7). Cheers, H. On 09/13/2017 02:54 PM, Ludwig Geistlinger wrote: Coercing vice versa, i.e. from SummarizedExperiment to ExpressionSet, which is defined in

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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,

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

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

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

An ExpressionSet is an eSet that is guaranteed to have an "exprs" assay. That makes no sense for example for methylation where we have (say) Green/Red assays or Meth/Unmeth assays (or transformations of these). Best, Kasper On Mon, Sep 11, 2017 at 3:31 PM, Ludwig Geistlinger <

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

Concerning 1) Why have some developers chosen to extend eSet instead of ExpressionSet: As far as I understand it, ExpressionSet was thought to exclusively represent a microarray experiment (MIAME = Minimum Information About a Microarray Experiment). Thus, back in the days when more and more

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

On Mon, Sep 11, 2017 at 2:02 PM, Hervé Pagès wrote: > Hi, > > I added coercion from ExpressionSet to SummarizedExperiment in > SummarizedExperiment 1.7.6. > Thank you Hervé! > The current behavior of the SummarizedExperiment() constructor > when called on a ExpressionSet

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

Hi, I added coercion from ExpressionSet to SummarizedExperiment in SummarizedExperiment 1.7.6. The current behavior of the SummarizedExperiment() constructor when called on a ExpressionSet object doesn't make much sense to me. I'd rather have it consistent with what the coercion does. Will fix

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

It's probably good keeping coercion and construction distinct, although we have violated that recently with GRanges(). It now attempts to coerce its first argument to a GRanges. Don't want to derail the discussion, but it's another data point. Michael On Mon, Sep 11, 2017 at 9:26 AM, Levi

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

On Mon, Sep 11, 2017 at 11:56 AM, Ludwig Geistlinger < ludwig.geistlin...@bio.ifi.lmu.de> wrote: > I guess we discussed this with Davide Risso @Bioc2017 in the > MultiAssayExperiment workshop. > > > SummarizedExperiment(mouseData) > > puts the eSet (rather counterintuitively) into `assays` of >

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

I guess we discussed this with Davide Risso @Bioc2017 in the MultiAssayExperiment workshop. > SummarizedExperiment(mouseData) puts the eSet (rather counterintuitively) into `assays` of `SummarizedExperiment`, it does not really coerce it to SummarizedExperiment, eg. `fData` and `pData` are not

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

Thanks Martin! I see the RangedSummarizedExperiment coercion method works when there are no mappable ranges (for example curatedMetagenomicData ExpressionSet objects), although the rowRanges is a GRangesList of empty elements. It might be worth also having a SummarizedExperiment coercion method it

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

On 09/10/2017 08:38 PM, Levi Waldron wrote: I just dug up this old thread because I realized we still don't have a coercion method as(sample.ExpressionSet, "SummarizedExperiment"). Since we try as(sample.ExpressionSet, "RangedSummarizedExperiment"); see

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

I just dug up this old thread because I realized we still don't have a coercion method as(sample.ExpressionSet, "SummarizedExperiment"). Since we do have SummarizedExperiment(sample.ExpressionSet), could the coercion method also be added easily? > library(Biobase) > library(SummarizedExperiment)

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

Hi, Vince. Looks like a good start. I'd probably pull all the assays from ExpressionSet into SummarizedExperiment as the default, avoiding data coercion methods that are unnecessarily lossy. Also, as it stands, the assayname argument is not used anyway? Sean On Sat, Sep 20, 2014 at 10:38 AM,

Re: [Bioc-devel] coerce ExpressionSet to SummarizedExperiment

On 09/20/2014 10:43 AM, Sean Davis wrote: Hi, Vince. Looks like a good start. I'd probably pull all the assays from ExpressionSet into SummarizedExperiment as the default, avoiding data coercion methods that are unnecessarily lossy. Also, as it stands, the assayname argument is not used