error with identifyOverExpressedGenes(cellchat)

[sanskritidey]

options(stringsAsFactors = FALSE)

Set the full human ligand-receptor interaction database

CellChatDB.use <- CellChatDB.human

Using a subset of CellChatDB for cell-cell communication analysis

CellChatDB.use <- subsetDB(CellChatDB.human, search = "Secreted Signaling")

Add the Secreted Signaling database in the CellChat object

cellchat@DB <- CellChatDB.use

3.Subset and pre-processing the expression data

subset the expression data to use less RAM

cellchat <- subsetData(cellchat)

Pre-processing the expression data

cellchat <- identifyOverExpressedGenes(cellchat)
Error in (function (cond) : error in evaluating the argument 'x' in selecting a method for function 'rowSums': subscript out of bounds**
**
cellchat <- identifyOverExpressedInteractions(cellchat)
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s

Optional: project gene expression data onto protein-protein interaction (PPI)

str(cellchat)
Formal class 'CellChat' [package "CellChat"] with 15 slots
..@ data.raw : num[0 , 0 ]
..@ data :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
.. .. ..@ i : int(0)
.. .. ..@ p : int 0
.. .. ..@ Dim : int [1:2] 30606 0
.. .. ..@ Dimnames:List of 2
.. .. .. ..$ : chr [1:30606] "RP11-34P13.7" "RP11-34P13.8" "FO538757.2" "AP006222.2" ...
.. .. .. ..$ : NULL
.. .. ..@ x : num(0)
.. .. ..@ factors : list()
..@ data.signaling:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
.. .. ..@ i : int(0)
.. .. ..@ p : int 0
.. .. ..@ Dim : int [1:2] 689 0
.. .. ..@ Dimnames:List of 2
.. .. .. ..$ : chr [1:689] "TNFRSF18" "TNFRSF4" "TNFRSF14" "TNFRSF25" ...
.. .. .. ..$ : NULL
.. .. ..@ x : num(0)
.. .. ..@ factors : list()
..@ data.scale : num[0 , 0 ]
..@ data.project : num[0 , 0 ]
..@ images : list()
..@ net : list()
..@ netP : list()
..@ meta :'data.frame': 0 obs. of 1 variable:
.. ..$ labels: Factor w/ 8 levels "T cells","Tumor cells",..:
..@ idents :Formal class 'factor' [package "methods"] with 3 slots
.. .. ..@ .Data : int(0)
.. .. ..@ levels : chr(0)
.. .. ..@ .S3Class: chr "factor"
..@ DB :List of 4
.. ..$ interaction:'data.frame': 1199 obs. of 11 variables:
.. .. ..$ interaction_name : chr [1:1199] "TGFB1_TGFBR1_TGFBR2" "TGFB2_TGFBR1_TGFBR2" "TGFB3_TGFBR1_TGFBR2" "TGFB1_ACVR1B_TGFBR2" ...
.. .. ..$ pathway_name : chr [1:1199] "TGFb" "TGFb" "TGFb" "TGFb" ...
.. .. ..$ ligand : chr [1:1199] "TGFB1" "TGFB2" "TGFB3" "TGFB1" ...
.. .. ..$ receptor : chr [1:1199] "TGFbR1_R2" "TGFbR1_R2" "TGFbR1_R2" "ACVR1B_TGFbR2" ...
.. .. ..$ agonist : chr [1:1199] "TGFb agonist" "TGFb agonist" "TGFb agonist" "TGFb agonist" ...
.. .. ..$ antagonist : chr [1:1199] "TGFb antagonist" "TGFb antagonist" "TGFb antagonist" "TGFb antagonist" ...
.. .. ..$ co_A_receptor : chr [1:1199] "" "" "" "" ...
.. .. ..$ co_I_receptor : chr [1:1199] "TGFb inhibition receptor" "TGFb inhibition receptor" "TGFb inhibition receptor" "TGFb inhibition receptor" ...
.. .. ..$ evidence : chr [1:1199] "KEGG: hsa04350" "KEGG: hsa04350" "KEGG: hsa04350" "PMID: 27449815" ...
.. .. ..$ annotation : chr [1:1199] "Secreted Signaling" "Secreted Signaling" "Secreted Signaling" "Secreted Signaling" ...
.. .. ..$ interaction_name_2: chr [1:1199] "TGFB1 - (TGFBR1+TGFBR2)" "TGFB2 - (TGFBR1+TGFBR2)" "TGFB3 - (TGFBR1+TGFBR2)" "TGFB1 - (ACVR1B+TGFBR2)" ...
.. ..$ complex :'data.frame': 157 obs. of 4 variables:
.. .. ..$ subunit_1: chr [1:157] "INHBA" "INHA" "INHA" "IL12A" ...
.. .. ..$ subunit_2: chr [1:157] "INHBB" "INHBA" "INHBB" "IL12B" ...
.. .. ..$ subunit_3: chr [1:157] "" "" "" "" ...
.. .. ..$ subunit_4: chr [1:157] "" "" "" "" ...
.. ..$ cofactor :'data.frame': 31 obs. of 16 variables:
.. .. ..$ cofactor1 : chr [1:31] "FST" "BAMBI" "TIE1" "PTPRB" ...
.. .. ..$ cofactor2 : chr [1:31] "" "" "" "" ...
.. .. ..$ cofactor3 : chr [1:31] "" "" "" "" ...
.. .. ..$ cofactor4 : chr [1:31] "" "" "" "" ...
.. .. ..$ cofactor5 : chr [1:31] "" "" "" "" ...
.. .. ..$ cofactor6 : chr [1:31] "" "" "" "" ...
.. .. ..$ cofactor7 : chr [1:31] "" "" "" "" ...
.. .. ..$ cofactor8 : chr [1:31] "" "" "" "" ...
.. .. ..$ cofactor9 : chr [1:31] "" "" "" "" ...
.. .. ..$ cofactor10: chr [1:31] "" "" "" "" ...
.. .. ..$ cofactor11: chr [1:31] "" "" "" "" ...
.. .. ..$ cofactor12: chr [1:31] "" "" "" "" ...
.. .. ..$ cofactor13: chr [1:31] "" "" "" "" ...
.. .. ..$ cofactor14: chr [1:31] "" "" "" "" ...
.. .. ..$ cofactor15: chr [1:31] "" "" "" "" ...
.. .. ..$ cofactor16: chr [1:31] "" "" "" "" ...
.. ..$ geneInfo :'data.frame': 41787 obs. of 6 variables:
.. .. ..$ Symbol : chr [1:41787] "A1BG" "A1BG-AS1" "A1CF" "A2M" ...
.. .. ..$ Name : chr [1:41787] "alpha-1-B glycoprotein" "A1BG antisense RNA 1" "APOBEC1 complementation factor" "alpha-2-macroglobulin" ...
.. .. ..$ EntrezGene.ID : int [1:41787] 1 503538 29974 2 144571 144568 NA NA 3 127550 ...
.. .. ..$ Ensembl.Gene.ID: chr [1:41787] "ENSG00000121410" "ENSG00000268895" "ENSG00000148584" "ENSG00000175899" ...
.. .. ..$ MGI.ID : chr [1:41787] "MGI:2152878" "" "MGI:1917115" "MGI:2449119" ...
.. .. ..$ Gene.group.name: chr [1:41787] "Immunoglobulin like domain containing" "Antisense RNAs" "RNA binding motif containing" "C3 and PZP like, alpha-2-macroglobulin domain containing" ...
..@ LR :List of 1
.. ..$ LRsig:'data.frame': 0 obs. of 11 variables:
.. .. ..$ interaction_name : chr(0)
.. .. ..$ pathway_name : chr(0)
.. .. ..$ ligand : chr(0)
.. .. ..$ receptor : chr(0)
.. .. ..$ agonist : chr(0)
.. .. ..$ antagonist : chr(0)
.. .. ..$ co_A_receptor : chr(0)
.. .. ..$ co_I_receptor : chr(0)
.. .. ..$ evidence : chr(0)
.. .. ..$ annotation : chr(0)
.. .. ..$ interaction_name_2: chr(0)
..@ var.features : list()
..@ dr : list()
..@ options :List of 2
.. ..$ mode : chr "single"
.. ..$ datatype: chr "RNA"
cellchat <- projectData(cellchat, PPI.human)
Error in solve.default(AA, BB) : no right-hand side in 'b'

[sqjin]

@sanskritidey Can you show your object@data.signaling and unique(object@idents)?