count_mtx choose for integrated Seurat object data

[Lawwwwo]

Hi! I am using SCEVAN to analyze an integrated Seurat object. I have no idea which count_mtx data should I choose from my Seurat object. There are three versions: RNA, SCT(transformed version), and integrated as the figure inserted below. When I choose RNA's matrix as input, it can run normally. But when I choose integrated it shows errors: The number of elements of the gene set is less than the minimum allowed. Error in hclust(d, method = "ward.D2") : NA/NaN/Inf in foreign function call (arg 10) Calls: <Anonymous> ... classifyTumorCells -> removeSyntheticBaseline -> hclust In addition: Warning messages: 1: In sqrt(count_mtx_proc) : NaNs produced 2: In sqrt(count_mtx_proc + 1) : NaNs produced Execution halted And screen output stops here: [1] " raw data - genes: 5000 cells: 13546" [1] "1) Filter: cells > 200 genes" [1] "low data quality" [1] "2) Filter: genes > 5% of cells" [1] "4935 genes past filtering" [1] "3) Annotations gene coordinates" [1] "found 0 confident non malignant cells" [1] "4797 genes annotated" [1] "4) Filter: genes involved in the cell cycle" [1] "4465 genes past filtering " [1] "5) Filter: cells > 5genes per chromosome " [1] "6) Log Freeman Turkey transformation" [1] "A total of 13546 cells, 4465 genes after preprocessing" [1] "7) Measuring baselines (pure tumor - synthetic normal cells)" And here is the code with using integrated code: Integrationdata_123M_CNV <- SCEVAN::pipelineCNA(Integrationdata_123M@assays[["integrated"]]@data, sample = "BreastCancerIntegration", par_cores = 80, SUBCLONES = FALSE, plotTree = FALSE) Can you help me figure out this problem? And which input should I choose?

[Lawwwwo]

Hi Antonio! I just tried another integration method with my data. The same problem occurs which stops at step 7) Measuring baseline: