I need a suggestion for batch variation for edgeR analysis.
Here is my samples
After plot MDS for NW1,NW2 and NW3, I choose to take NW1 and NW3 as they are similar more than NW2.
Similarly, I have another set of sample NWS1, NWS2, NWS3. After Plot MDS, I have taken NWS1 and NWS3 for the DE using EdgeR
but my plot MDS for NW1, NW3, NWS1 and NWS3 look weird. As NW1 is quite away from the NW3. Any suggestion for this batch effects.
Thanks a million