Error in `Idents<-`: ! 'value' must be a factor or vector

XIANZHE-LI commented 2 months ago

nichenet_output_agnostic <- nichenet_seuratobj_aggregate(

seurat_obj = DCM,
sender = "undefined",
receiver = "CM",
condition_colname = "group",
condition_oi = "DCM",
condition_reference = "healthy donor",
expression_pct = 0.05,
ligand_target_matrix = ligand_target_matrix,
lr_network = lr_network,
weighted_networks = weighted_networks,
top_n_ligands = 80,
top_n_targets = 500,
lfc_cutoff = 0.1,
assay_oi = "RNA"
) [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 Idents<-: ! 'value' must be a factor or vector

seurate V5

ShiweiHePH commented 1 month ago

I also found this problem(seurate V5)

[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 Idents<-: ! 'value' must be a factor or vector

csangara commented 1 month ago

Hi,

Can both of you check that your NicheNet version is 2.1.5? This issue should have been fixed in #198, but it's possible that I overlooked some lines of code.

XIANZHE-LI commented 1 month ago

Hi,

Can both of you check that your NicheNet version is 2.1.5? This issue should have been fixed in #198, but it's possible that I overlooked some lines of code.

saeyslab / nichenetr

Error in `Idents<-`: ! 'value' must be a factor or vector #284