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

[Charles Plessy]

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

-- 
Charles Plessy - - ~ ~ ~ ~ ~ ~~~~ ~ ~ ~ ~ ~ - - charles.plessy using oist.jp
Okinawa  Institute  of  Science  and  Technology  Graduate  University
Staff scientist in the Luscombe Unit - ~ - https://groups.oist.jp/grsu
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