When I run lapply to normalise, scale, etc. my seurat objects I get an error.
Code:
singlecell.object.list <- lapply(X = singlecell.object.list, FUN = function(x){
x <- NormalizeData(x)
x <- FindVariableFeatures(x, selection.method = "vst", nfeatures = 1000)
x <- ScaleData(x,features = VariableFeatures(x))
x <- RunPCA(x, features = VariableFeatures(object = x))
x <- FindNeighbors(x, dims = seq(10))
x <- FindClusters(x, resolution = 0.1)
})
Error:
Computing nearest neighbor graph
Computing SNN
Error in validityMethod(as(object, superClass)) :
object 'CsparseMatrix_validate' not found
Hi Oscar, I'm Jose.
When I run lapply to normalise, scale, etc. my seurat objects I get an error. Code: singlecell.object.list <- lapply(X = singlecell.object.list, FUN = function(x){ x <- NormalizeData(x) x <- FindVariableFeatures(x, selection.method = "vst", nfeatures = 1000) x <- ScaleData(x,features = VariableFeatures(x)) x <- RunPCA(x, features = VariableFeatures(object = x)) x <- FindNeighbors(x, dims = seq(10)) x <- FindClusters(x, resolution = 0.1) }) Error: Computing nearest neighbor graph Computing SNN Error in validityMethod(as(object, superClass)) : object 'CsparseMatrix_validate' not found
Attached is my script. Thanks. ClusterFoldSimilarity_GEO_datasets.txt