How to find DEG with deseq2 in R

Question

[mresmaeili995]

I have downloaded a dataset(GSE98622) from GO databases. This data is best suited for my experiences, and I need to extract DEG from it, but this data is normalized and I can't use it. What should I do in this situation?

AKI <- read.table("GSE98622a.txt", sep = "\t")
x <-as.matrix(AKI)
rownames(x)<-x[,1]
x <- x[,-1]
AKI <- as.data.frame(x)
class(AKI)
gr <- c(rep("n", 17), rep("C", 16), rep("d", 16))
colData <- data.frame(group=gr, type="paired-end")
cds <- DESeqDataSetFromMatrix(data.matrix(AKI), colData, design = ~group)
resLFC.AKI <- data.frame(lfcShrink(data.matrix(AKI), coef="group_d_vs_n"))

Many thanks

[Marco Pannone]

Did you get a matrix of already normalized read counts? What type of normalization has been used?

[mresmaeili995]

Matrix array but also we need numeric data type

The error is:

> cds <- DESeqDataSetFromMatrix(data.matrix(AKI), colData, design = ~group)
Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
> resLFC.AKI <- data.frame(lfcShrink(data.matrix(AKI), coef="group_d_vs_n"))
Error in lfcShrink(data.matrix(AKI), coef = "group_d_vs_n") : 
  is(dds, "DESeqDataSet") is not TRUE

[ATpoint]

Read the DESeq2 manual. Your entire code is wrong, manual will instruct you.