I have three groups (with multiple replicates each) from 3 different locations. How can I obtain the DEG between the three groups since I have no control to compare to? I would like to obtain a list of the DEG across samples, and then run pairwise tests ANOVA + posthoc of specific genes between the three regions.
Would this be the way? Is there a better of more efficient way of doing this?
dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ region)
# ANOVA anova <- aov(df_genes$Value ~ df_genes$Region) summary(anova) # Tukey test tuckey.test<- TukeyHSD(anova) tuckey.test