I'm using TCGA Lung cancer data. I'm interested in doing differential analysis between Lung vs Normal. Before DEA, to check the distance between each pair of samples I plotted an MDS plot:
In this, I see some Tumor samples are clustered with Normals. As this is a two dimensional plot, it is a little hard to say.
So, I made a clustering heatmap with the top 10% genes:
My question is: Should I exclude those tumor samples which are clustering with the normals for differential analysis? Is it a good idea to remove samples based on clustering?
Note: I didn't see any technical bias of those samples