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How to calculate the mitochondrial percent in GSE124395? #4

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hahmu opened this issue Feb 27, 2024 · 0 comments
Open

How to calculate the mitochondrial percent in GSE124395? #4

hahmu opened this issue Feb 27, 2024 · 0 comments

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@hahmu
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hahmu commented Feb 27, 2024

Hello,

Thank you very much for your amazing works!
I downloaded the GSE124395 and copy your code:
##Aizarani
data<-readRDS('GSE124395_Normalhumanliverdata.RData')
aizarani_healthy<-CreateSeuratObject(data, project="Aizarani_Healthy", min.cells=3, min.features = 300)
VlnPlot(aizarani_healthy, features = c("nFeature_RNA", "nCount_RNA"), ncol = 2)
aizarani_healthy[["percent.mt"]] <- PercentageFeatureSet(aizarani_healthy, pattern = "^MT-")
aizarani_healthy <- subset(aizarani_healthy, subset = nFeature_RNA > 300 & nFeature_RNA < 2500 & percent.mt < 30)

But while checking with violin plot, all cells have percent.mt = 0.
Can you help me to deal with this problem?
Thank you very much!

Ha

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