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Comparing transcriptomes of 3 samples

Hello! I am comparing the transcriptomes of 3 types of cells, I'll call them A1, A2 and B for convenience. What would be the best way to see the relationship between the transcriptomes (i.e which 2 populations have the most variance and which 2 populations have the least variance and so on)? I did the PCA analysis and all replicates related to each of the samples cluster together and PC1 (44%) shows more variance between A1 and B, while PC2 (26%) shows some variance between A1 and A2 but it is difficult to make any inferences if the transcriptomes of A1 and A2 have more similarities or A1 and B have more similarities. I wanted to do a venn diagram but wasn't sure how to approach this, since there's no control/stem cell population to compare A1, A2, B. If anyone has any suggestions that would be much appreciated.

Thank you!

rna-seq venn diagram
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written by snp87 • snp87

Comparing transcriptomes of 3 samples

The title of this post makes it sounds like you want to compare the sequence content of 3 transcriptomes but then the body of the post appears to referring to comparison of gene expression. Please change the title of the post to accurately reflect the question.

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written by GenoMax GenoMax

What will just looking at the variance show? It may provide something interesting but absolutely nothing on which solid conclusions could be made.

Perhaps you may just do something like this:

  1. normalise your data
  2. transform to logged counts
  3. transform to Z-scores
  4. set |Z|>3 for expressed/not expressed in each cell
  5. create a Venn diagram from the resulting lists [of expressed / not-expressed]
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written by Kevin Blighe Kevin Blighe

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