I've used DESeq2 to analyse a few RNA-Seq samples. I followed pretty closely the manual and using the following code
I created the following PCA plot:
What I don't understand is - what are the units that are recorded on the x/y axes? What's their meaning?
Code:
vsd <- varianceStabilizingTransformation(dds) data <- plotPCA(vsd, intgroup=c("condition"), returnData=TRUE) percentVar <- round(100 * attr(data, "percentVar")) plotPCA <- ggplot(data, aes(PC1, PC2, color=condition)) + geom_point(size=3) + xlab(paste0("PC1: ",percentVar[1],"% variance")) + ylab(paste0("PC2: ",percentVar[2],"% variance")) + geom_text(aes(label=names),hjust=0.25, vjust=-0.5, show_guide = F) ggsave("PCA.pdf", plot = plotPCA)
What I don't understand is - what are the units that are recorded on the x/y axes? What's their meaning?
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