The Net contain nothing

[cynthier]

Hi, I analyzed the stereo-seq (bin30) data and infered the neuron communication. Evey step seems smoothly, but it yields nothing. Could you please help me?

CellChatDB <- subsetDB(CellChatDB, 
                     search = "Non-protein Signaling", 
                     key = "annotation")

scale.factors = list(tol = 7.5, ratio = 0.5)
cellchat <- createCellChat(object = count, 
                           meta = meta, 
                           group.by = "labels",
                           datatype = "spatial", ###
                           coordinates = spatial.locs, 
                           scale.factors = scale.factors)

cellchat <- computeCommunProb(cellchat, 
                              type = "truncatedMean", 
                              trim = 0.05, 
                              raw.use = TRUE,
                              population.size = TRUE,
                              distance.use = TRUE,
                              scale.distance = 0.05,
                              k.min = 5,
                              contact.knn.k = 6,
                              interaction.range = 50, # Unit: microns
                              nboot = 20,
                              contact.knn.forced = TRUE
                             )

truncatedMean is used for calculating the average gene expression per cell group. [1] ">>> Run CellChat on spatial transcriptomics data using distances as constraints of the computed communication probability <<< [2023-12-22 16:11:33]" The suggested minimum value of scaled distances is in [1,2], and the calculated value here is 1.227142 [1] ">>> CellChat inference is done. Parameter values are stored in object@options$parameter <<< [2023-12-22 16:11:38]"

[UmaSangumathi]

Hi, I have the same issue. How was this solved? Thanks

[cynthier]

@UmaSangumathi It may indicate there no LRs detected? Since it worked when I change the DB used.