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It seems here that regression works successfully. But when i try the exact same steps on my data I get no differences, not even a slight change.
Below you can see the respective plots on my data but i am only showing 2 as the before and after regression are the exact same plots.
My data with no difference of before and after regression:
As you can see, especially in the first PC (PC1) it is explained by mostly the cc genes which i want to regress out.
I also searched this before opening a discussion here and the only thing i found is if the cc genes exist in my data. I can confirm that the cc genes do exist in my data. Finally i have observed that the marrow data has 774 cells and 23035 genes while my data has 31782 cells (from 2 samples) and 21601 genes. Could this be issue? and if yes how do i fix it?
Can someone please help me and explain what does this mean and how to fix it?
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Hello everyone. I have a question regarding the SCTransform in seurat.
Below are the exact steps I did using the data from here https://satijalab.org/seurat/articles/cell_cycle_vignette.html
library(Seurat)
exp.mat <- read.table(file = "/mnt/nfs_IKLomics/nestorawa_forcellcycle_expressionMatrix.txt",
header = TRUE, as.is = TRUE, row.names = 1)
sgenes <- cc.genes$s.genes
g2m <- cc.genes$g2m.genes
marrow <- CreateSeuratObject(counts = Matrix::Matrix(as.matrix(exp.mat), sparse = T))
marrow <- SCTransform(marrow)
marrow <- RunPCA(marrow)
marrow <- CellCycleScoring(marrow, s.features = sgenes, g2m.features = g2m)
marrow <- RunPCA(marrow, features = c(sgenes, g2m))
k2 = dfHeatCor(marrow)
corrplot(k2)
DimPlot(marrow,reduction = "pca",group.by = "Phase")
Before regression:
marrow = SCTransform(marrow,vars.to.regress = c("S.Score", "G2M.Score"))
marrow <- RunPCA(marrow, features = c(sgenes, g2m))
l=dfHeatCor(marrow)
corrplot(l)
DimPlot(marrow,reduction = "pca",group.by = "Phase")
After regression:
It seems here that regression works successfully. But when i try the exact same steps on my data I get no differences, not even a slight change.
Below you can see the respective plots on my data but i am only showing 2 as the before and after regression are the exact same plots.
My data with no difference of before and after regression:
As you can see, especially in the first PC (PC1) it is explained by mostly the cc genes which i want to regress out.
I also searched this before opening a discussion here and the only thing i found is if the cc genes exist in my data. I can confirm that the cc genes do exist in my data. Finally i have observed that the marrow data has 774 cells and 23035 genes while my data has 31782 cells (from 2 samples) and 21601 genes. Could this be issue? and if yes how do i fix it?
Can someone please help me and explain what does this mean and how to fix it?
Thank you all :)
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