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Hi guys,
I'm confusing about how is the difference between principle component plot (PCA) and multi-dimension scaling plot (MDS). I have six RNA-Seq samples with three replications for two treatments. My PC plot was constructed by WGCNA package and MDS by edgeR.
As so far I noticed, PCA seems to be unnormalized and MDS is normalized. Am I correct? And could anyone share the difference between these two plots? And which should I use for publishing?
Thank you
I'm confusing about how is the difference between principle component plot (PCA) and multi-dimension scaling plot (MDS). I have six RNA-Seq samples with three replications for two treatments. My PC plot was constructed by WGCNA package and MDS by edgeR.
As so far I noticed, PCA seems to be unnormalized and MDS is normalized. Am I correct? And could anyone share the difference between these two plots? And which should I use for publishing?
Thank you