Can I compare different RNAseq experiment DEG lists to see which experiments are the most similar?
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4 weeks ago

Hi all, Is it possible to compare the differentially expressed genes from different RNAseq datasets to see which experimental conditions produce the most significantly similar expression changes in genes? I have 3 individual experiments (2 different conditions in each):

  1. M1

1.2. M1 + compound

  1. M2

2.2. M2 + compound

  1. M3

3.2. M3 + compound

I want to see which experimental conditions produce the most statistically similar DEGs. If anyone could advise that would be great. Thank you!

DEG lists Comparision RNAseq • 269 views
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Before looking at the DEGs, I would suggest starting with a PCA plot and/or the euclidean distance between the samples. This will give you a good idea globally which samples are most similar.

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Hi and thanks for the reply! Would you recommend performing the PCA on normalised counts? thanks!

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Yea, I would run the PCA using the normalized counts. That would reduce the influence of library size and the mean-variance relationship which aren't interesting for this analysis.

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