Normalize: 比值中位数法

过程: https://zhuanlan.zhihu.com/p/521724558
原理: https://cloud.tencent.com/developer/article/2031932; https://www.jianshu.com/p/fc19ff2d3721; https://www.zhangshilong.cn/work/326289.html

1. 代码

require(DESeq2)

kk <- read.table("/home/zhiyong/Work/Data/BulkRNA-seq/Amel/Date_from_SRA/PRJNA470779/Counts_all_of_Drone_Queen_Worker.txt")

sample <- factor(c("Drone","Drone","Drone","Queen","Queen","Queen","Worker","Worker","Worker"))

dds <- DESeqDataSetFromMatrix(kk, DataFrame(sample), design= ~ sample )

dds<-estimateSizeFactors(dds)

sizeFactors(dds.sizefactor )     查看标准化因子

normalized_counts<-counts(dds,normalized=TRUE)     生成 normalize 以后的表达矩阵