Question: How To Extract Proteins Representing Time Points In Time Course Principal Component Analysis
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gravatar for The
5.2 years ago by
The100
United States
The100 wrote:

I'm trying to do a PCA analysis for a time course protein expression study and for three time points. I wish to find out proteins that best represents the time points.In other words I wish to get a list of proteins which appear in different "sectors" of time as given in this example plot/link.

PCA analysis of the time course response to benomyl of the wild type strain

I used the following R script for doing the PCA and generate the Biplot.

rm(list=ls())
my.df <- read.table("expression_log2ratio.txt",row.names=1,header=TRUE,sep="\t",check.names=FALSE)
prot.pca <- prcomp(na.omit(my.df), scale=FALSE)  
summary(prot.pca)
biplot(prot.pca,col=c("blue","red"),cex=c(0.5,0.5)    )

My input data is of the folllowing format with around 4000 proteins. The numerical values are that of log2ratios

    T1    T2    T3
p1    -0.071396303    0.006385917    0.088535769
p2    -0.115839104    0.043409057    -0.035812972
p3    -0.01593602    -0.02627361    0.014833213
.....

My Biplot looks as follows: MyPcaBiplot

Can anybody suggest how to extract the proteins in different 'sectors' using R ? Any help is highly appreciated.

pca • 1.9k views
ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by The100
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