Seurat: NormalizeData()

1. NormalizeData()

method = LogNormalize :

• 1. Feature counts for each cell are divided by the total counts for that cell
• 2. Multiplied by the scale.factor (10000)
• 3. Log1p()

结果存放在 @assays$RNA@data 中

2. NormalizeData(Seurat_object, assay = "HTO", normalization.method = "CLR")

https://zhuanlan.zhihu.com/p/477173992

对 HTO 数据进行 CLR 归一化处理

对Seurat_object@assays$HTO@counts中的每一行进行CLR处理，即对同一hashtag的UMI值在细胞之间进行归一化

归一化后的值放在 Seurat_object@assays$HTO@data 中

处理步骤：

kk <- as.numeric(kk@assays$HTO@counts[1,])
data_0 <- log1p(kk[kk > 0])
data_1 <- sum(data_0, na.rm=TRUE)
data_2 <- length(kk)
data_3 <- exp(data_1/data_2)
data_4 <- kk/data_3
log1p(data_4) : CLR 归一化后的值