Question: Selecting Samples based on Clustering
0
gravatar for rajpal22288
9 days ago by
rajpal2228850
Germany
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

Heatmap-Most-Var2

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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