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saeyslab / nichenetr

NicheNet: predict active ligand-target links between interacting cells
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there is a warning in this shetp-"score ligand-receptor interactions based on expression strength of the receptor" #240

Open GGboy-Zzz opened 7 months ago

GGboy-Zzz commented 7 months ago

Hi, when I ran "the differential_nichenet_pEMT vignettes“，I found a warning in the step, code as follows,

exprs_sender_receiver <- lr_network_dr %>%

  • inner_join(exprs_tbl_ligand, by = c("ligand")) %>%
  • inner_join(exprs_tbl_receptor, by = c("receptor")) %>% inner_join(DE_sender_receiver %>% distinct(niche, sender, receiver)) Joining with by = join_by(sender, receiver) Warning messages: 1: In inner_join(., exprs_tbl_ligand, by = c("ligand")) : Detected an unexpected many-to-many relationship between x and y. ℹ Row 1 of x matches multiple rows in y. ℹ Row 1 of y matches multiple rows in x. ℹ If a many-to-many relationship is expected, set relationship = "many-to-many" to silence this warning. 2: In inner_join(., exprs_tbl_receptor, by = c("receptor")) : Detected an unexpected many-to-many relationship between x and y. ℹ Row 1 of x matches multiple rows in y. ℹ Row 342 of y matches multiple rows in x. ℹ If a many-to-many relationship is expected, set relationship = "many-to-many" to silence this warning. Will this have any impact on the results?