Open hjack123 opened 4 years ago
No it’s raw count
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On Sep 26, 2019, at 6:15 PM, hjack123 notifications@github.com wrote:
before applying FindTransferAnchors, is the gene activity matrix being normalized?
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Thank you! and when making the gene/peak activity matrix, were they preselected by the promoter region?
The peak or gene region is customized and you can choose to use any regions or promoters. The gene.bed file used in the demo are all genes. For integration, only variable genes identified using RNA seq are used for analysis.
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On Sep 27, 2019, at 11:10 AM, hjack123 notifications@github.com wrote:
Thank you! and when making the gene/peak activity matrix, were they preselected by the promoter region?
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Hi, thank you so much for replying again!! Is the weight reduction also using LSI?
No. It uses the diffusion maps
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On Sep 27, 2019, at 2:01 PM, hjack123 notifications@github.com wrote:
Hi, thank you so much for replying again!! Is the weight reduction also using LSI?
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Dear all,
And how about the gene expression matrix? is it normalized before Transfer anchors or raw count?
And for gene activity matrix, which one is used (from Cicero or the simple one in Seurat tutorial)?
Thank you
Dear all,
And how about the gene expression matrix? is it normalized before Transfer anchors or raw count?
And for gene activity matrix, which one is used (from Cicero or the simple one in Seurat tutorial)? @hjack123 @r3fang Thank you
before applying FindTransferAnchors, is the gene activity matrix being normalized?