ERROR in less than 3 samples (basic_analysis_steps_MISC_SACL.knit.md). ERROR: get_DE_info_sampleAgnostic #80
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contrasts_oi = c("'P-(A+B+C+D+T)/5','A-(P+B+C+D+T)/5','B-(A+P+C+D+T)/5','C-(A+B+P+D+T)/5','D-(A+B+C+P+T)/5','T-(A+B+C+D+P)/5'")
contrast_tbl = tibble(contrast =
c("P-(A+B+C+D+T)/5","A-(P+B+C+D+T)/5", "B-(A+P+C+D+T)/5","C-(A+B+P+D+T)/5","D-(A+B+C+P+T)/5","T-(A+B+C+D+P)/5"),
group = c("P","A","B","C","D","T"))
senders_oi = SummarizedExperiment::colData(sce)[,celltype_id] %>% unique()
receivers_oi = SummarizedExperiment::colData(sce)[,celltype_id] %>% unique()
sce = sce[, SummarizedExperiment::colData(sce)[,celltype_id] %in%
c(senders_oi, receivers_oi)
]
conditions_keep =c("P","A","B","C","D","T")
sce = sce[, SummarizedExperiment::colData(sce)[,group_id] %in%
conditions_keep
]
DE_info = get_DE_info_sampleAgnostic(
sce = sce,
group_id = group_id, celltype_id = celltype_id,
contrasts_oi = contrasts_oi,
expressed_df = frq_list$expressed_df,
min_cells = min_cells,
contrast_tbl = contrast_tbl)
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:
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