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Cannot find the following identities in the object: Other #305

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arunchakra opened this issue Sep 27, 2024 · 0 comments
Open

Cannot find the following identities in the object: Other #305

arunchakra opened this issue Sep 27, 2024 · 0 comments

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@arunchakra
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Hello I am running the standard Niche Net pipeline and following this vignette:
https://github.com/saeyslab/nichenetr/blob/master/vignettes/seurat_wrapper.md

I am getting an issue when running this portion:
nichenet_output_agnostic <- nichenet_seuratobj_aggregate(
seurat_obj = seuratObj,
sender = "G_180-315",
receiver = "S_180-315",
condition_colname = "Niche",
condition_oi = "180-315",
condition_reference = "Other",
expression_pct = 0.05,
ligand_target_matrix = ligand_target_matrix,
lr_network = lr_network,
weighted_networks = weighted_networks
)

[1] "The RNA assay will be used for the analysis."
[1] "Read in and process NicheNet's networks"
[1] "Define expressed ligands and receptors in receiver and sender cells"
[1] "Perform DE analysis in receiver cell"
Error in WhichCells.Seurat(object = object, idents = ident.2) :
Cannot find the following identities in the object: Other

The condition column, Niche has the following values 180 -315 and Other:

table(seuratObj$Niche)

180-315 Other
64154 128219

Meanwhile the senders and recievers are in a different column that is set to the identity of the Seurat object. This should be just like the vignette so I am confused by this error. Could you please help if you have an idea?

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