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Monocle 3 batch correction error #722

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ZFMZSR opened this issue May 20, 2024 · 0 comments
Open

Monocle 3 batch correction error #722

ZFMZSR opened this issue May 20, 2024 · 0 comments
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@ZFMZSR
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ZFMZSR commented May 20, 2024

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

@ZFMZSR ZFMZSR added the bug Something isn't working label May 20, 2024
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