**10**wrote:

Hi,

For RNASeq analysis, I am generating a PCA plot for various strains with three biological replicates each. When I make the PCA plot , I get a symbol on the plot for every replicate. For a large dataset, I was wondering if there is a way to have a single symbol (average of three biological replicates) be represented on the plot, instead of all three replicates.

In DESeq2 package I use:

library(ggplot2)

data <- plotPCA(rld, intgroup=c("clade", "strain"), returnData=TRUE)

percentVar <- round(100 * attr(data, "percentVar"))

ggplot(data, aes(PC1, PC2, color=strain, shape=clade)) +

geom_point(size=3) +

xlab(paste0("PC1: ",percentVar[1],"% variance")) +

ylab(paste0("PC2: ",percentVar[2],"% variance")) +

coord_fixed()

Thanks,

Priyanka

**26k**• written 2.8 years ago by pkachroo •

**10**