I have metagenome samples from 24 animals. and for each animal, the samples were taken from three different locations (Ileum, Caecum and Colon). I tested the effect of three treatments (8 animals/treatment) on the metagenome level and Now I want to use DESeq2 tool to find the specific genes that are significantly affected by treatment per gut section. For example Effect of treatment, A compared to Treatment B in Ileum.
Therefore, I used DESeq2 with the following design:
dds$group <- factor(paste0(dds$gutsection, dds$treatment)) design(dds) <- ~ group dds <- DESeq(dds) So my questions are 1. Is this a correct design? resultsNames(dds) results(dds, contrast=c("group", "Ile.TreatmentB", "Ile.TreatmentA"))
2. The above design works fine with no error. However, when I subset the data per gut section and run a DESeq2 analysis with this design; (ILE_dataset,~ Treatment), I get different results! Is not that strange? I saw a post from a while ago with a similar question but I am not sure if this is the right explanation also in my case. http://seqanswers.com/forums/showthread.php?t=48354
I'd appreciate any comments and explanation.