Hi everyone,

I am doing a PCA analysis with my RNASeq data and I want to konw whether the genotypes have a great effect on the gene expression. I have four genotypes :G0(wild type),G1,G2,G3 and three time points: T1,T2,T3. All the values in the dataset are Log2FC values compared to wild type. The data looks like this:

Hi Aaron, thanks for your reply. The dot in my description of the data means the value, I did not give the actual value for each datapoint, just use dot instead.

The command I used to generate the PCA plot is as follows:

library(psych)
library(GPArotation)
data = read.table("C:\\Users\\Desktop\\PCA\\log2FC.csv", header=T, sep = ",")
attach(data)
str(data)
Datax = prcomp(data[,-1], retx=TRUE, center=TRUE,scale= TRUE)
str(Datax)
summary(Datax)
scores <- Datax$x
scores
sd <- Datax$sdev
loadings <- Datax$rotation
loadings[1:3,]
write.csv(loadings, "C:\\Users\\Desktop\\PCA\\pca.csv")
g <- ggbiplot(Datax,groups=Genotype,var.axes=FALSE,scale=1)
print(g)

Following is the picture of the PCA plot