I am trying to make a group-wise comparison between 4 groups using DESeq2. After writing the contrast for the group comparisons, I see that log2foldchange and the lfcSE are different for each comparison but values for stat and p-value are the same for each comparison. Eg: Group1_vs_Group2 has the same P-values and stat as Group1_vs_Group3. I don't think this is correct. I'd really appreciate it if you could look at it and let me know if I am making a mistake with model building for any other thing.
library(DESeq2) Pheno <- read.csv('xxxxxxx.csv', header=T,sep=",") Data <- read.csv('yyyyyyy.csv', header=T,row.names=1) Pheno$Position <- as.character(Pheno$Position) Data <- Data[,Pheno$Position] dds <- DESeqDataSetFromMatrix(countData = Data, colData = Pheno, design = ~ Groups) #design(dds) = ~ Groups dds = DESeq(dds, test = "LRT", reduced = ~ 1) group1_group2 <- results(dds, contrast=c("Groups", "Group1", "Group2")) group1_group2 <- group1_group2[!is.na(group1_group2$pvalue),] group1_group2 <- group1_group2[order(group1_group2$pvalue), decreasing = T] group1_group3 <- results(dds, contrast=c("Groups", "Group1", "Group3")) group1_group3 <- group1_group3[!is.na(group1_group3$pvalue),] group1_group3 <- group1_group3[order(group1_group3$pvalue), decreasing = T]