New to bioconductor & DESeq2. I have trying to look into the differential expression of primary tumor vs matched normal tumors. My question is that once I run the analysis & print a MA-plot I seem to have way to many differentially expressed genes. Is there any command of function that I may be missing in my analysis?
dds <- DESeqDataSetFromMatrix(countData=cts, colData=colData, design= ~ condition) ddsf <- estimateSizeFactors(dds) ddsf$condition <- relevel(dds$condition,ref='NT') dds <- DESeq(dds) res <- results(dds, contrast=c('condition','MPT', 'NT')) plotMA(dds,ylim=c(-5,5),main="Ma-Plot")