Closed twfs closed 3 years ago
Hi Tim,
Sorry for the late reply. It appears that the error is caused by irregularities in your object:
> str(rowData(rds))
Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
..@ rownames : chr [1:18620] "TSPAN6" "TNMD" "DPM1" "SCYL3" ...
..@ nrows : int 18620
..@ listData :List of 4
.. ..$ gene : chr [1:18620] "TSPAN6" "TNMD" "DPM1" "SCYL3" ...
.. ..$ gene.mean : num [1:18620] NA NA NA NA NA NA NA NA NA NA ...
.. ..$ gene.dispersion : num [1:18620] NA NA NA NA NA NA NA NA NA NA ...
.. ..$ gene.dispersion.scaled: num [1:18620(1d)] NA NA NA NA NA NA NA NA NA NA ...
.. .. ..- attr(*, "dimnames")=List of 1
.. .. .. ..$ : chr [1:18620] NA NA NA NA ...
..@ elementType : chr "ANY"
..@ elementMetadata: NULL
..@ metadata : list()
Notice that "$ gene.dispersion.scaled: num [1:18620(1d)] NA NA NA NA NA NA NA NA NA NA ...
" is not a vector but a 1d array.
Make sure you install the latest sceasy
code, and do
rds@rowRanges@elementMetadata@listData$gene.dispersion.scaled <- as.vector(rds@rowRanges@elementMetadata@listData$gene.dispersion.scaled)
before converting, and it should work.
Thanks for the fix. These objects were constructed using the SCE conversion methods in a previous Seurat package version. This may have been a bug in Seurat that has now been fixed, will try some more recent objects and see if that works.
Thanks again,
Tim
Hi, thanks for SCEasy! I'm trying to convert from a single cell experiment to AnnData and get:
Error in dn[[2L]] : subscript out of bounds Calls: ... .local -> lapply -> lapply -> FUN -> colnames -> colnames
In addition: Warning message:
In .regularise_df(as.data.frame(SummarizedExperiment::colData(obj))) :
Dropping single category variables:orig.ident
Execution halted
Example SCE RDS file attached: EC_sce.zip
Thanks for any help,
Tim