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Are these samples good enough for DEA analysis?

Hi all, Are these samples good enough for DEA analysis? Because I think the tumor and normal samples are not well separated.

enter image description here Here is my code:

NormalizedCounts.scaled <- t(scale(t(NormalizedCounts) , scale = F))
pc <- prcomp(NormalizedCounts.scaled)

pcr <- data.frame(pc$rotation[,1:3] , Group = gr) 
ggplot(pcr, aes(PC1 , PC2 , color = Group)) + geom_point()

Thanks for any help.

pca rna-seq
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written by Azade • Azade

This is an awesome separation for clinical data, you will often just see a mess of points with no separation at all because of all the potential confounders in human specimen that obscure the actual clinical effect you're after. Go ahead, plug into your favourit DE software and see what comes out.

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written by ATpoint ATpoint

Thanks for your positive feedback.

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written by Azade • Azade

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