Description:
I’m trying to perform batch correction using Monocle 3, but I’m getting the following error when calling align_cds():
cds = align_cds(cds, alignment_group ="orig.ident")
Aligning cells from different batches using Batchelor.
Please remember to cite:
Haghverdi L, Lun ATL, Morgan MD, Marioni JC (2018). 'Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.' Nat. Biotechnol., 36(5), 421-427. doi: 10.1038/nbt.4091
Error in L1[[i]] : this S4 class is not subsettable
In addition: Warning messages:
1: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = TRUE.
2: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = TRUE.
3: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = TRUE.
4: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = TRUE.
5: In class(x) <- unique.default(c("AsIs", oldClass(x))) :
Setting class(x) to multiple strings ("AsIs", "SimpleIntegerList", ...); result will no longer be an S4 object
6: In class(x) <- unique.default(c("AsIs", oldClass(x))) :
Setting class(x) to multiple strings ("AsIs", "SimpleIntegerList", ...); result will no longer be an S4 object
7: In class(x) <- unique.default(c("AsIs", oldClass(x))) :
Setting class(x) to multiple strings ("AsIs", "SimpleDFrameList", ...); result will no longer be an S4 object
Description: I’m trying to perform batch correction using Monocle 3, but I’m getting the following error when calling align_cds():