Seurat, FIndVariableFeatures(): vst not implemented yet

Question

[Hatchet]

Hello,

I downloaded a single cell dataset from GEO (147424). The samples are gunzipped comma separated txt files (rows = genes, columns = cells) . Read in the files with read.table:

S1_LES <- read.table("./GSE147424_RAW/uncompressed_txt_counts/S1_LS/GSM4430459_MS.sample1.clean.data.txt", header = T, sep = ",", dec = ".", row.names = 1)

...

Created the seurat objects:

S1_LES_SO <- CreateSeuratObject(counts = S1_LES, min.cells = 3, min.features = 200)

...

started to do integration. When i ran this:

sample_SO_names <- c("S1_LES_SO", "S2_LES_SO", "S3_NL_SO", "S4_HC_SO", "S5_LES_SO", "S6_HC_SO", "S7_LES_SO", "S8_HC_SO", "S9_HC_SO", "S10_HC_SO", "S11_NL_SO", "S12_HC_SO", "S13_HC_SO", "S14_NL_SO", "S15_NL_SO", "S16_NL_SO", "S17_HC_SO")
seuratObj_list1 <- mget(sample_SO_names)

performLogNorm <- function(seuratObj){
  seuratObj <- NormalizeData(object = seuratObj)
  seuratObj <- FindVariableFeatures(seuratObj, selection.method = "vst", nfeatures = 2000)
  return (seuratObj)
}
sample_list_qc <- mapply(FUN = performLogNorm, seuratObj = seurat_list1, SIMPLIFY = FALSE)

I got an error:

Probably it has to do with the data being just one file. Usually i just give the folder path for the Read10X function and it's good to go. While reading in with read.table:

Thank you for any help.

Answer 1

[Hatchet]

Meantime managed to solve this. The problem was that i created the seurat object from the dataset matrices directly that was downloaded. So when it showed that "Counts matrix provided is not sparse" i had to convert this into a sparse matrix. First into a matrix because it was read in as a dataframe and then into a sparse matrix with the "Matrix" package:

S1_LES <- as.matrix(S1_LES)
  S1_LES <- Matrix(S1_LES, sparse = TRUE)

After this it went through integration without any problem.