#快速找出所有细胞类型的差异/Marker基因

Rscript $scripts/seurat_FindAllMarkers.r --rds $workdir/05.cell_type_ann/pbmc.added.celltype.rds \

 -p FindAllMarkers --test.use  DESeq2   --logfc.threshold 0.25 ，执行此代码后报错：Warning: When testing 20 versus all:

every gene contains at least one zero, cannot compute log geometric means

Warning: When testing 21 versus all:

every gene contains at least one zero, cannot compute log geometric means

Warning: When testing 22 versus all:

every gene contains at least one zero, cannot compute log geometric means

Warning: When testing 23 versus all:

every gene contains at least one zero, cannot compute log geometric means

Warning: When testing 24 versus all:

every gene contains at least one zero, cannot compute log geometric means

data frame with 0 columns and 0 rows

Error in `group_by_prepare()`:

! Must group by variables found in `.data`.

• Column `cluster` is not found.

Backtrace:

    ▆

 1. ├─obj.markers %>% group_by(cluster) %>% ...

 2. ├─dplyr::top_n(., n = opt$top_n, wt = avg_log2FC)

 3. │ └─dplyr::filter(...)

 4. ├─dplyr::group_by(., cluster)

 5. └─dplyr:::group_by.data.frame(., cluster)

 6.   └─dplyr::group_by_prepare(.data, ..., .add = .add, caller_env = caller_env())

 7.     └─rlang::abort(c("Must group by variables found in `.data`.", glue("Column `{unknown}` is not found.")))

Execution halted

想问下是我输入文件的问题还是？我从第一部开始就是按照视频中的课程操作的？麻烦老师解答。谢谢老师