Open tian6067 opened 1 month ago
The previous codes can all run normally, but an error occurs when calculating differentially expressed genes (get_DE_info_sampleAgnostic).
The detail information : sce: class: SingleCellExperiment dim: 15611 200474 metadata(0): assays(2): counts logcounts rownames(15611): A4GALT AAAS ... ZZEF1 ZZZ3 rowData names(0): colnames(200474): AAACCCAAGAGTGTGC-1_1 AAACCCAAGCACCAGA-1_1 ... TTTGTTGTCCTCTGCA-1_17 TTTGTTGTCGTTCTAT-1_17 colData names(16): orig.ident nCount_RNA ... cell ident reducedDimNames(1): PCA.FULL mainExpName: RNA altExpNames(0):
sample_id = "orig.ident"
group_id = "time" table(sce$time) A B C D P T 32108 29129 38452 33829 33313 33643
celltype_id = "cell" table(sce$cell) CEC LEC AT1 AT2 BASEL CIL GC SC TC AM B BPLA CD4 CD8 DC 6428 545 18701 101362 1873 5578 0 3958 1085 7714 3089 1610 9690 4268 0 MAST MON NEUT FIB MES SMC 848 14810 10777 2200 1303 4635
covariates = NA batches = NA
frq_list$expressed_df
celltype gene expressed
Hi @tian6067
as a test: can you check whether running the DE analysis on your data works if you would only compare 2 conditions?
eg
contrasts_oi = c("'P-A','A-P'"
bug information: Error in assign(".effective_grid", effective_grid, envir = envir) : 'envir' Incorrect parameters
but it has something wrong when i run above code , i don't konw which step is wrong.can you help me to solve it issue: