Selecting Samples based on Clustering
If I only select samples based on their clustering in heatmaps, am I not creating a bias ? For example, I had 35 samples (RNA Seq) nitially, but, in the end, we only selected 12 samples based on their clustering. When I checked for some of the genes in both cases, they were hugely varying in terms of P-adjusted value.
I mean, I know this is a bias but how do I explain this to my boss? Please Helpppp!!!
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Can you give us some information on what the samples are, your method for clustering, and how clusters were selected?
So, there were 3 types of samples.
Performed Correlation clustering after DESEQ2 using Pheatmap
Now, let's say, only violet samples with large cluster was selected, and the cyan cluster was completely removed from the final analysis.