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

[XIANZHE-LI]

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]

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]

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]

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.

[Shubhra1994]

same issue here!

[csangara]

I still can't figure out what's going wrong here. If anyone could provide me with the following, it will be very helpful.

• Their sessionInfo()
• The version of their Seurat object: seuratObj@version
• The exact line the code malfunctions when following the step-by-step vignette