Closed browaeysrobin closed 1 year ago
No problem -- just be aware: if using findMarkers = TRUE, you need to provide a contrast_tbl as argument (this is now specified in the error message in the function in release version 2 -- currently on devel-branch, later main branch)
DE_info_FM = get_DE_info(sce, sample_id, group_id, celltype_id, batches, covariates, contrasts_oi, min_cells = 10, assay_oi_pb = "counts", fun_oi_pb = "sum", de_method_oi = "edgeR", findMarkers = TRUE, contrast_tbl = contrast_tbl, filterByExpr.min.count = 7, filterByExpr.min.total.count = 15, filterByExpr.large.n = 4, filterByExpr.min.prop = 0.7)
See issues #12 and #13 : bug in code of
get_DE_info
when optionfindMarkers = TRUE