Seurat - Warning after rescaling a subset of the data

Question

[Assa Yeroslaviz]

After sub-setting my data set I reapeat the workflow of Normalization -> Find-HVG -> ScaleData

But for some reason I get this warning.

Warning: Different features in new layer data than already exists for scale.data

I know it is only a warning, but I want to make sure, I don't work on the wrong assay as I have several assays.

thank you

Answer 1

[Bastien Hervé]

The reason is that by subsetting your object you obtain different HVG than with your full object. You have run ScaleData on your full object with your HVG (by default 2000 genes), which is the default behaviour of ScaleData. When you ran it a second time on your object subset, your list of HVG is different, thus, the error message. You can ignore the warning, the scale.data matrix is gonna be replace.