I'm trying to plot a distribution graph of the gene expression values,after and before normalization, from microarray data.
Here is my code to obtain a plot of the normalized values,
library(Biobase) library(GEOquery) library(magrittr) library(rJava) library("xlsx") library(stringr) library(ggplot2) eset <- getGEO('GSE20966')[] boxplot(exprs(eset), outline=FALSE) edata <- data.frame(exprs(eset)) ggplot(eset[,1])
I expected to obtain a plot similar to the distribution plot shown at the end of the page in this tutorial
Unfortunately, I couldn't succeed in doing this. Could someone suggest if there are alternate ways of plotting the logged gene expression values of each sample?(I expect a normally distributed plot)