Simple version: calculating norm

##Deseq2 making a normalized count data for raw counts
##1/Download DESeq2
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("DESeq2")
BiocManager::install("IRanges")
library(DESeq2)


##2/input data
MD.RNA.count <- read.csv(file.choose(), row.names = 1)
View(MD.RNA.count)
anno <- read.csv(file.choose(), row.names = 1)
anno <- anno[,c("class1","class2","class3")]
View(anno)
MD.RNA.matrix <- as.matrix(MD.RNA.count)


##3/dds
dds <- DESeqDataSetFromMatrix(countData = MD.RNA.matrix, colData = anno, design = ~ class3)

DESeq(dds)
head(counts(dds))
dds <- estimateSizeFactors(dds) 
MD_RNA_normal2 <- counts(dds, normalized=TRUE)
write.csv(MD_RNA_normal2,file = "pool_gene_RNA_normalized.csv")