I'm working with 10X scRNASeq data and the Surface Markers data that come with it.
I'm having issues integrating the two datasets, I'm following what suggested in the Multimodal Vignette (https://satijalab.org/seurat/v3.0/multimodal_vignette.html).
more specifically:
mat <- Read10X(data.dir = matrix_dir)
# mat[[1]] will have RNA and mat[[2]] will have proteins
list_RNA <- CreateSeuratObject(counts = mat[[1]], project = nn, min.cells = 3, min.features = 200)
list_RNA[["percent.mt"]] <- PercentageFeatureSet(list_RNA, pattern = "^MT-")
list_RNA[[nn]] <- nn
list_RNA <- subset(list_RNA, subset = nFeature_RNA > 200 & nFeature_RNA < 2500 & percent.mt < 5)
list_RNA <- NormalizeData(list_RNA, normalization.method = "CLR", scale.factor = 10000, assay = "RNA")
list_RNA <- FindVariableFeatures(list_RNA, selection.method = "vst", nfeatures = 2000)
list_RNA <- ScaleData(list_RNA)
# now to integrate the data:
list_RNA[["Proteins"]] <- CreateAssayObject(mat[[2]])
but I get
Error: Cannot add a different number of cells than already present
any suggestions?
I'm working with 10X scRNASeq data and the Surface Markers data that come with it. I'm having issues integrating the two datasets, I'm following what suggested in the Multimodal Vignette (https://satijalab.org/seurat/v3.0/multimodal_vignette.html). more specifically:
but I get
Error: Cannot add a different number of cells than already present
any suggestions?