SummarizedExperiment

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loading package taking too much memory

2

SummarizedExperiment is using too much memory and time to load. The code bellow and results indicate that it is taking 328MB of memory. For a single use this is not...

spocks

In the _CAGEr_ package I use a `SummarizedExperiment` object to store `DataFrame`s of `Rle`-encoded expression values. Updating the objects give warnings such as `The dim() method for DataFrameList objects is...

charles-plessy

colData Default in Constructor Inconsistency

1

Is `DataFrame()` but perhaps ought to be `NULL` for consistency with `rowData`.

DarioS

There are a few use cases where you might want to be able to combine `SummarizedExperiment` "by assay", which can be thought of as combining along the Z axis in...

multimeric

package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'SummarizedExperiment'

1

I get the error: Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to...

bakaufman

Hello, @catiapacifico opened an issue to our framework that is utilizing SummarizedExperiment. https://github.com/microbiome/OMA/issues/202 This is quite rare case, but I thought that it is worth to let you know since...

TuomasBorman

I'm not quite sure why I did this, but the current code at https://github.com/Bioconductor/SummarizedExperiment/blob/8df97720354bdeecaf947f574dddd09da02d55b2/R/combine-methods.R#L244 wipes out the names of the metadata list, e.g., ```r example(SummarizedExperiment, verbose=FALSE) metadata(se)

LTLA

Enforce unique assay names

2

This started as a more general discussion about [empty strings in List names](https://github.com/Bioconductor/S4Vectors/issues/47) but the real concern seems to be more specifically about the names of the assays. It comes...

hpages

Should the show() method for SummarizedExperiment objects suggest saveHDF5SummarizedExperiment()?

1

Vince (@vjcitn) suggested: > One could imagine the show method for SummarizedExperiment checking to see if there is evidence of HDF5 in the assay and if it finds it, it...

hpages

rowData rownames issue explored at BioC2018

6

Here is a reproducing example for a potential issue in the devel branch version of SummarizedExperiment. It seems an inconsistency in rownames of rowData and rownames of the SE, which...

mikelove