I have a question about an output file I have created using the programme edgeR. I am somewhat familiar with genomics processing, but am trying to work with some tools I have never used before. My analysis is on an RNA sequencing dataset with three caategories (day 1, day 3, day 6), with 3 replicates each, so 9 samples in total. I have run every step until the differentially expressed genes analysis, which I have set up both in edgeR and in DEseq2 to compare the two.
I have questions about the output of both, but for now I would like to ask just one thing.
In edgeR, my output, (edgeR report in the history tab) shows me an MDS plot, shown below. I have a vague idea of what an MDS plot is, but mostly because I have had PCA covered in a statistics course, whereas MDS is actually PCoA.
I can see that the day 1 samples (in green) group nicely. However, for the day 3 and day 6 samples, only 2 of of 3 group separately whereas for both groups 1 sample (day3 R3 and day6 R3 in figure) do not group as well.
I am not 100% certain if I performed my analysis correctly, but assuming I did, I would like to ask for some advice on how to continue with my data. Would it invalidate my data if I removed the R3 replicates of day 3 and day 6 that group separate from the pairs of other replicates? Or would it be fine to do this?