Error in (function (cl, name, valueClass) : "data" is not a slot in the "Assay5" category.

[Pigeongeon]

【code】：
library(Libra)
OnlyTumor_HCC_atlas$MLGS_Group <- factor(OnlyTumor_HCC_atlas$MLGS_Group,levels = c("High","Low"))
DE2 = run_de(
OnlyTumor_HCC_atlas,
meta = meta.data,
replicate_col = NULL,
cell_type_col = "Release_Global_Cluster",
label_col = "MLGS_Group",
min_cells = 3,
min_reps = 2,
min_features = 0,
de_family = "singlecell",
de_method = "wilcox"
)

【Bug】：
Error in (function (cl, name, valueClass) :
"data" is not a slot in the "Assay5" category.

[haukeh90]

Hi,

I think the problem lies within the V5 Seurat assay that needs to be converted prior to run_de.

convert a v3 assay to a v5 assay

pbmc3k[["RNA5"]] <- as(object = pbmc3k[["RNA3"]], Class = "Assay5")

Afterwards you need to set the RNA3 assay as DefaultAssay.

Best,

Hauke

[Random-x-1]

expr_mtx_com is a dgCMatrix with features (genes) in rows and cells in columns.
meta_data_com is a matched dataframe metadata

single_de_results <- Libra::run_de(
input = expr_mtx_com,
meta = meta_data_com,
label_col = label_col,
replicate_col = "SubjectID",
cell_type_col = "cell_types",
min_cells = 1,
min_reps = 2,
de_family = "singlecell",
de_method = "wilcox",
n_threads = 56)

Still got following error:
Error in (function (cl, name, valueClass) :
"data" is not a slot in the "Assay5" category.

[AlanTeoYueYang]

Hi, you can try running this command to see if there's any change in the input given into the de function
inputs = Libra:::check_inputs(input = expr_mtx_com, meta = meta_data_com, ...)