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glados 04-22-2014 03:42 AM

cummeRbund PCA plot
Can anyone explain cummeRbund's PCA plot?
I posted this question earleir in the RNA-sequencing forum but never got any replies so will try here in the Bioinformatics forum.

I do understand traditional PCA plots, like the one in DESeq, and cummeRbund's MDS plot, but what does everything in cummeRbund's PCA version mean? What are the dots (PCA loading factors or expression values?), and what are the arrows? (There is no explanation in the manual)

TiborNagy 04-22-2014 04:45 AM

Dots are expression values transformed into PC. The arrows show how depends the given condition to the PC (you can see axes rotations.)

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