I pulled down two h5ad files from https://developmental.cellatlas.io/fetal-bone-marrow.
(1) Human fetal BM 10x dataset and (2) Human fetal BM Down syndrome 10x dataset)
The Down syndrome data loads fine using MuDataSeurat::ReadH5AD. The typical data set gives me this error.
d21 <- MuDataSeurat::ReadH5AD("/tmp/fig1b_fbm_scaled_gex_updated_dr_20210104.h5ad")
Warning: Feature names cannot have underscores (''), replacing with dashes ('-')
Error in (function (cl, name, valueClass) :
assignment of an object of class “dgCMatrix” is not valid for @‘scale.data’ in an object of class “Assay”; is(value, "matrix") is not TRUE
In addition: Warning message:
In read_layers_to_assay(h5) :
The var_names from modality have been renamed as feature names cannot contain ''. E.g. RP11-442N24__B.1 -> RP11-442N24--B.1.
I pulled down two h5ad files from https://developmental.cellatlas.io/fetal-bone-marrow.
(1) Human fetal BM 10x dataset and (2) Human fetal BM Down syndrome 10x dataset)
The Down syndrome data loads fine using MuDataSeurat::ReadH5AD. The typical data set gives me this error.