Hello, guys, I have a problem getting the DEseq2 normalized value. I am using R4.3.2 and DESeq2 version 1.42.0. I have 32 samples for 4 groups. The raw count data is obtained from Hisat2-string tie pipeline. I would like to get DESeq2 normalized value, but only A1 sample value did not change from the raw count. Could anyone tell me how to resolve this? Do I make the wrong data. frame?

Thanks, Shitetsu

My code is below.

x<-read.table("Book14.txt",sep = "\t", header = T, row.names = 1, quote="")
is.data.frame(x)
x <- as.matrix(x)
coldata <- data.frame(sample = c("A1","A2","A3","A4","A5","A6","A7","A8","B1","B2","B3","B4","B5","B6","B7","B8","C1","C2","C3","C4","C5","C6","C7","C8","D1","D2","D3","D4","D5","D6","D7","D8"), condition = c("A","A","A","A","A","A","A","A","B","B","B","B","B","B","B","B","C","C","C","C","C","C","C","C","D","D","D","D","D","D","D","D"), row.names = "sample")
dds <- DESeqDataSetFromMatrix(countData = x, colData = coldata, design = ~ condition)
dds <- estimateSizeFactors(dds)
NC <- counts(dds, normalized=TRUE)
head(NC)

And the this is the capture of x and NC

What is the output of sizeFactors(dds)?