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Dear team, thank you for your wonderful software RISC. It is great!
However, I run umap and find the clusters crowd together and overlap (pic in the attachment)
And the code below (scRNA is my Seurat object with four batches day0, day2, day5, and day14.)
Thank you!
Hi Roger, sorry to reply a little late, I check the issue periodically.
Usually, we do not evaluate other groups' analyses, because people can use the codes and paramters they want. Here I want to remind you two things:
(1) in functions {scMultiIntegrate, scUMAP, scCluster}, it is better to use the same number of PCs, eigens == npc (scUMAP) == npc (scCluster). This is just based on my experience.
(2) I suggest you change your code about variable genes (also based on my exprience):
From var0 = Reduce(intersect, list(dat0@rowdata$Symbol, dat2@rowdata$Symbol, dat5@rowdata$Symbol, dat14@rowdata$Symbol))
To var0 = unique(c(dat0@vargene, dat2@vargene, dat5@vargene, dat14@vargene)) length(var0)
if length(var0) around 5000, I will use this.
Dear team, thank you for your wonderful software RISC. It is great!
However, I run umap and find the clusters crowd together and overlap (pic in the attachment)
And the code below (scRNA is my Seurat object with four batches day0, day2, day5, and day14.)
Thank you!
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