Entering edit mode
11 weeks ago
Assa Yeroslaviz
★
1.9k
When I subset a seurat object and start to reanalyze it, I can't change the number of variable features from the older (bigger object).
seuObj
An object of class Seurat
26379 features across 56411 samples within 1 assay
Active assay: RNA (26379 features, 2000 variable features)
3 layers present: data, counts, scale.data
3 dimensional reductions calculated: pca, umap, tsne
After subsetting and cleaning the object, I re-do also the normalization and finding the variable features, but it stays at 2000, even though I can see in the plot, that I have a lot more.
export <- subset(x = seuObj, idents = c(1,2,11) )
export <- NormalizeData(export, normalization.method ="LogNormalize", scale.factor = 10000)
export <- FindVariableFeatures(export, selection.method = "mean.var.plot", mean.cutoff = c(0.0125, 3), dispersion.cutoff = c(0.5, Inf))
export
An object of class Seurat
26379 features across 13384 samples within 1 assay
Active assay: RNA (26379 features, 2000 variable features)
2 layers present: counts, data
How can I reset (change)this value?
It might just be an issue of update in the printing of the class Seurat
Double check the actual number of variable features you actually have in the object
Did you find a workaround for this?