Seurat: errors when runing RunPCA

Created on 1 Aug 2019  路  1Comment  路  Source: satijalab/seurat

When I run
klf5_d2 <- RunPCA(klf5_d2, features = VariableFeatures(object = klf5_d2))
the error is : Error in irlba(A = t(x = object), nv = npcs, ...) :
max(nu, nv) must be strictly less than min(nrow(A), ncol(A))

the number of cells is 42, the number of features is 20239.
When i use the data having 95 cells , it works well. So, Is it because there are so few cells?

Most helpful comment

The default number of PCs to compute is 50, so you are trying to find more components than there are cells. You need to set npcs to less than the smallest dimension of the dataset

>All comments

The default number of PCs to compute is 50, so you are trying to find more components than there are cells. You need to set npcs to less than the smallest dimension of the dataset

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