getting Error in pca_current[, seq_len(10)] : subscript out of bounds

[MartinLoza]

Hi, I am trying to integrate two PBMC batches (control and stimulation) but keep getting the same error. And example of what I am trying to do is:

`library(Seurat)
library(SeuratData)
library(scMerge)

if (! "ifnb" %in% SeuratData::InstalledData()[["Dataset"]]) {
SeuratData::InstallData("ifnb")
}
Uncorrected <- SeuratData::LoadData("ifnb")
Uncorrected <- NormalizeData(Uncorrected, verbose = FALSE)
Uncorrected <- FindVariableFeatures(Uncorrected,
nfeatures = 2000,
verbose = FALSE)

features <- VariableFeatures(Uncorrected)

Correction <- as.SingleCellExperiment(Uncorrected[features,])

Correction <- scMerge(sce_combine = Correction,
ctl = features,
kmeansK = c(3,3),
batch_name = "stim",
assay_name = "scMerge",
plot_igraph = FALSE)`

I am interested in correcting only the variable features, so I subset as Uncorrected[features,]
I have tried different ways to create the SingleCellObject but keep getting the same error. It is worth to note that I don't get the error if I dont't subset the Uncorrected batch.
Thanks in advance for any suggestion you may have.

[grimwoo]

Hi, @MartinLoza
I had exactly same error. Have you solved this one?