Closed pcm32 closed 3 years ago
Parsing the object in R via readRDS()
and then getting its attributes causes the following:
> query_sce
class: SingleCellExperiment
dim:
metadata(5): neighbors pca raw.var raw.X louvain
Error in getClass(element.type) : “SimpleAssays” is not a defined class
hmm, I am having the same error querying the content of your rds file. However, https://humancellatlas.usegalaxy.eu/datasets/11ac94870d0bb33a005bfb8cba4fb8dd/stdout seems to suggest the rds is normal under sceasy_convert
's container environment. I also tried running the conversion code in my local environment using the input loom and I can read normally the content of the converted rds in the same environment. My guess is that the bioconductor/SingleCellExperiment versions are different/incompatible between sceasy_convert
and scmap_preprocess_sce
.
Input dataset: https://humancellatlas.usegalaxy.eu/datasets/11ac94870d0bb33a4d823102dcb034bc/display?to_ext=loom
Result dataset was specifically https://humancellatlas.usegalaxy.eu/datasets/11ac94870d0bb33a005bfb8cba4fb8dd/display?to_ext=rdata (although it is an RDS, long story).
Entire history here: https://humancellatlas.usegalaxy.eu/u/pmoreno/h/atlas-scanpy-scmap-e-geod-94641-2
Will add more details on the R part.