[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

[Hervé Pagès]

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
>
> SummarizedExperiment/R/makeSummarizedExperimentFromExpressionSet.R
>
> as follows:
>
> setAs("SummarizedExperiment", "ExpressionSet", function(from)
>      as(as(from, "RangedSummarizedExperiment"), "ExpressionSet")
> )
>
> also seems to be a bit problematic, as it makes you lose your rowData/fData.
>
>
>
> Here is an example:
>
> ## Constructing the SE similar to examples of ?SummarizedExperiment
>> nrows <- 200; ncols <- 6
>> counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
>> colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
>                            row.names=LETTERS[1:6])
>
>
> ## some rowData with simulated gene IDs
>> rowData <- DataFrame(EntrezID=sample(1000, 200), row.names=paste0("g",
> 1:200))
>> se <- SummarizedExperiment(assays=SimpleList(exprs=counts),
>                              colData=colData, rowData=rowData)
>
> # this is how it looks
>> rowData(se)
> DataFrame with 200 rows and 1 column
>       EntrezID
>      <integer>
> 1         289
> 2         476
> 3         608
> 4         998
> 5         684
> ...       ...
> 196       331
> 197       590
> 198       445
> 199        95
> 200       129
>
> (why did I actually lost the rownames g1-g200 here?)
>
>
> ## Coercing to Expression makes me losing the rowData/fData
>> eset <- as(se, "ExpressionSet")
>> fData(eset)
> data frame with 0 columns and 200 rows
>
>
> ## So where is the problem?
> ## Apparently in the coercion
> ##    from SummarizedExperiment to RangedSummarizedExperiment
>> rse <- as(se, "RangedSummarizedExperiment")
>> rowData(rse)
> DataFrame with 200 rows and 0 columns
>
>

-- 
Hervé Pagès

Program in Computational Biology
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