different group for the same predicted cell in GeneIntegrationMatrix

[Zepeng-Mu]

Hi, I observed some strange behavior in the gene integration matrix results:

> scRNA$predicted.celltype.l2["HC1-PBMC_AACTCAGCACCACCAG-1"]
HC1-PBMC_AACTCAGCACCACCAG-1 
                  "B naive" 
> projCmb2$predictedGroup_Co[projCmb2$predictedCell_Co == "HC1-PBMC_AACTCAGCACCACCAG-1"]
  [1] "B intermediate" "B naive"        "B naive"        "B naive"        "B naive"        "B intermediate" "B intermediate" "B naive"        "B naive"        "B intermediate" "B naive"       
 [12] "B naive"        "B naive"        "B naive"        "B naive"        "B intermediate" "B intermediate" "B naive"        "B naive"        "B naive"        "B naive"        "B naive"       
 [23] "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B intermediate" "B naive"       
 [34] "B intermediate" "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B intermediate" "B naive"       
 [45] "B naive"        "B naive"        "B intermediate" "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"       
 [56] "B intermediate" "B naive"        "B naive"        "B naive"        "B intermediate" "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"       
 [67] "B naive"        "B intermediate" "B intermediate" "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"       
 [78] "B intermediate" "B intermediate" "B intermediate" "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"       
 [89] "B naive"        "B naive"        "B intermediate" "B intermediate" "B naive"        "B intermediate" "B naive"        "B naive"        "B naive"        "B naive"        "B naive"       
[100] "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B intermediate" "B naive"        "B naive"        "B naive"        "B intermediate"
[111] "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B intermediate" "B naive"        "B naive"        "B naive"        "B naive"       
[122] "B naive"        "B naive"        "B naive"        "B intermediate" "B naive"        "B naive"        "B memory"       "B naive"        "B naive"        "B intermediate" "B naive"       
[133] "B naive"        "B naive"        "B naive"        "B naive"        "B intermediate" "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"       
[144] "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B intermediate" "B naive"        "B intermediate" "B naive"        "B naive"       
[155] "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B intermediate" "B naive"        "B naive"       
[166] "B intermediate" "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B naive"       
[177] "B naive"        "B naive"        "B naive"        "B naive"        "B intermediate" "B naive"        "B intermediate" "B naive"        "B intermediate" "B intermediate" "B intermediate"
[188] "B intermediate" "B intermediate" "B naive"        "B intermediate" "B naive"        "B intermediate" "B naive"        "B naive"        "B intermediate" "B intermediate" "B naive"       
[199] "B naive"        "B intermediate" "B intermediate" "B naive"        "B naive"        "B naive"        "B naive"        "B naive"        "B intermediate" "B naive"        "B naive"       
[210] "B naive"        "B naive"        "B intermediate" "B intermediate" "B naive"        "B intermediate" "B naive"        "B naive"        "B intermediate" "B naive"        "B intermediate"
[221] "B naive"        "B naive"        "B naive"        "B intermediate" "B naive"        "B naive"        "B naive"        "B intermediate"

Basically, there is a B naive from scRNA dataset, and this cell mapped to many cells in scATAC dataset, but the label of these cells are B naive and B intermediate. I'm expecting these cell all have the same labels as "B naive". This is how I ran it:

projCmb2 <- addGeneIntegrationMatrix(
  ArchRProj = projCmb2, 
  useMatrix = "GeneScoreMatrix",
  matrixName = "GeneIntegrationMatrix",
  reducedDims = "ReducedMNN50",
  seRNA = scRNA,
  addToArrow = T, 
  groupList = groupListNew,
  groupRNA = "predicted.celltype.l2",
  dimsToUse = 1:50,
  corCutOff = 0.75,
  scaleDims = T,
  nameCell = "predictedCell_Co",
  nameGroup = "predictedGroup_Co",
  nameScore = "predictedScore_Co",
  threads = 4,
  force = T
)