[Bioc-devel] EXTERNAL: MultiAssayExperiment silently converting RangedSummarizedExperiments into SummarizedExperiments.

Hi Charles,

Thank you for your post and for providing a reproducible example.

I was able to reduce the example to behavior from the coerce method on
`list`/`ANY` objects to `SimpleList`.

Here is the reduced example:

``` r
suppressPackageStartupMessages({
 ??? library(SummarizedExperiment)
})
example(SummarizedExperiment, echo = FALSE)
mylist <- list(exo1 = rse, exo2 = se0)

simple <- as(mylist, "SimpleList")

simple[[1]]
#> class: SummarizedExperiment
#> dim: 200 6
#> metadata(0):
#> assays(1): counts
#> rownames: NULL
#> rowData names(1): feature_id
#> colnames(6): A B ... E F
#> colData names(1): Treatment

vapply(simple, class, character(1L))
#>?????????????????? exo1?????????????????? exo2
#> "SummarizedExperiment" "SummarizedExperiment"
```

<sup>Created on 2019-09-03 by the [reprex
package](https://urldefense.proofpoint.com/v2/url?u=https-3A__reprex.tidyverse.org&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=9duQHKmIe42r7lOJQrxpEAIYslget3GtzOUH_7YsQ-o&s=q8UONw1z3Bk43KNBDbmA-m1gBE1J7l6w3McrPDDaTfU&e= ) (v0.3.0)</sup>

It appears that `S4Vectors:::coerceToSimpleList` looks for the
`S4Vectors:::lowestListElementClass` and coerces all classes in the list
to be the base `SummarizedExperiment` class. I'm not sure what the
reasoning is behind the behavior.

Can you chime in Herv?? Thanks.

- Marcel



On 8/28/19 1:28 AM, Charles Plessy wrote:

Hello,

I am using MultiAssayExperiment as a base class in the CAGEr package.

In Bioconductor 3.10, CAGEr is broken because updates of
RangeSummarizedExperiment experiments trigger their silent conversion
to SummarizedExperiment objects (basically discarding the ranges).  This
only happens when there is another experiment slot that contains a plain
SummarizedExperiment.

Here is a toy example to reproduce the issue:

```{r}
library("MultiAssayExperiment")
(DF       <- DataFrame(sample1=c(1,2), sample2=c(1,3)))
(rRanges  <- GPos("chr1", 1:2, "+"))
(cData    <- DataFrame(type=c("control", "treatment"), row.names =
c("sample1", "sample2")))
(rSE      <- SummarizedExperiment(SimpleList(DF), rowRanges = rRanges,
colData = cData))
(SE       <- SummarizedExperiment(SimpleList(DF), colData = cData))
(m        <- MultiAssayExperiment(ExperimentList(exp1=rSE)))
(m[[1]]   <- m[[1]])
m # No change
(m        <- c(m, exp2=SE))
(m[[1]]   <- m[[1]])
m # RangedSummarizedExperiment replaced with SummarizedExperiment
sessionInfo()
```

Am I misusing the MultiAssayExperiment objects, or is this a bug ?

Have a nice day,

Charles

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