DESeq2 code to perform DEG analysis
library(DESeq2)
rawCountTable <- as.matrix(read.delim(file.choose(), row.names=1))
Col_data = read.table(file = "ANN_LUAD.txt", header = T, sep = "\t")
dds <- DESeqDataSetFromMatrix(countData = rawCountTable, colData = Col_data, design = ~ Type)
dds = DESeq(dds)
keep <- rowSums(counts(dds)) >= 10
dds <- dds[keep,]
dds = estimateSizeFactors(dds)
sizeFactors(dds)
vsd <- assay(varianceStabilizingTransformation(dds, blind=FALSE))
After this I have done the gene mapping and I want to ask the next step with the codes to get DEGs result
https://drive.google.com/file/d/118nDashzRA7hyVLUmUsot2CEquxuEaZB/view?usp=share_link
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issue with the codes how to do the next step
Put your data away for a few days and go through a DESeq2 tutorial or two first.
Everything you need to know is in the DESeq2 vignette so take time to read about it : http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html