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cannot find dispersion value in HVFInfo(seu)

Open Jiayi-Zheng opened this issue 6 months ago • 0 comments

Sorry this is a very naive question but I couldn't seem to find the answer. I was analysing a spatial seq dataset whose pca explains very limited variance. So I decided to look back at genes. I got a standard variance (y-axis) vs average expression (x-axis) plot via VariableFeaturePlot(seu) and I was able to obtain the mean, variance and variance.standardized of each gene via HVFInfo(seu). Then I was trying to reference back to a previous scRNA-seq dataset I analyzed, of which when I do VariableFeaturePlot(seu) I got a dispersion (y-axis) vs average expression (x-axis) plot. This time the HVFInfo(seu) returned my a dataframe with mean, dispersion, dispersion.scaled of each gene. The only difference I could think of is that I was using Seurat V4 when analyzing the previous dataset, and now i'm using seurat V5.

Is there a way for me to get the dispersion values and plot in seurat V5? I couldn't seem to find it when searching with all the keywords I could think of.

Thank you!

Jiayi-Zheng avatar Aug 13 '24 05:08 Jiayi-Zheng