Question: Selecting Samples based on Clustering
gravatar for rajpal22288
9 days ago by
rajpal2228850 wrote:

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!!!

sequencing rna-seq gene • 56 views
ADD COMMENTlink modified 9 days ago • written 9 days ago by rajpal2228850

Can you give us some information on what the samples are, your method for clustering, and how clusters were selected?

ADD REPLYlink written 9 days ago by rpolicastro4.0k

So, there were 3 types of samples.

  1. Treated Nodules - 16 samples
  2. Control Nodules - 3 samples
  3. Untreated Nodules - 16 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.

ADD REPLYlink modified 9 days ago • written 9 days ago by rajpal2228850
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