Error in Seurat ScaleData() function

Question

[bioinformatics.girl]

Hey, so I have been having a recurring error for the past week to no avail. Once I perform "FindVariableFeatures()" on a SeuratObject, I get the error:

seurat_object$var.genes<- FindVariableFeautres(seurat_object, selection.method = "vst", nfeatures = 4000)

"Error in ``[<-.data.frame(*tmp*``, , i, value = new("Seurat", assays = list( : replacement has 32285 rows, data has 38328"

I have also looked on the Seurat forum on GitHub, and again not much help. Looking for any input which is much needed. Thank you!

[Ram]

Please use a code block to paste your code and error. Using inline code doesn't work when the error has back-ticks in it.

Copy and paste the command and error message again, include a blank line at the end. Select all of it then click the 101010 button.

Answer 1

[ATpoint]

Assign the output directly to the Seurat object, not to $…, the method puts the output where it needs to be automatically. Follow the guided tutorials on the Seurat website if you’re new to it.

[bioinformatics.girl]

Thank you so much for your helpful input ATpoint! Simple yet effective and worked!

[GenoMax]

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