Question: Seurat3 DimPlot inconsistency
gravatar for mbk0asis
5 weeks ago by
Korea, Republic Of
mbk0asis560 wrote:

Hi, all!

I'm currently analysing a single cell RNA-seq data using Seurat3.

While analysing, I found that the UMAP/tSNE plots by DimPlot kept changing everytime I ran it even though I sat the seed.use for RunPCA and RunUMAP.

The code I used is below.

>nDim = 50
>mipsc <- RunPCA(mipsc, npcs = nDim, features = VariableFeatures(object = mipsc), seed.use = 123)
>ElbowPlot(mipsc, ndims = nDim)
>mipsc <- RunUMAP(mipsc, dims = 1:20, seed.use = 123) 

Is there a bug in the code or other steps I must set a seed?

Thank you!

seurat rna-seq seurat3 • 73 views
ADD COMMENTlink written 5 weeks ago by mbk0asis560


My version of Seurat is 3.1.5. In the docs of runPCA() and runUMAP says: seed.use: Set a random seed. By default, sets the seed to 42. Setting NULL will not set a seed.. By default is using the seed 42, so there is no need to set the seed at all in first place (I mean, if you just want to keep reproducibility).

This seems odd to me. Therefore, you might consider open an issue on their github repo:


ADD REPLYlink written 5 weeks ago by antonioggsousa870

Thank you, António!

I will do that~~

ADD REPLYlink written 5 weeks ago by mbk0asis560
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