InvitroMacrophagePCRanalysis

This is an R Markdown document to analyze qPCR data from an experiment which tests if SHH can further enhance the expression of cytokines (IL-12, IL-1β, CXCL-2 and TNF) in H. pylori stimulated macrophages. Control gene: HPRT.

if (getwd() != "/Users/shruti/Dropbox/shrutim/Rscripts/qPCR/MacrophagePcr")
  {
    setwd(file.path(getwd(),"Dropbox","SHRUTIM","Rscripts","qPCR","MacrophagePcr"))
  }
pcr_data <- read.csv("./invitro_WT_03082014_analysis_V2.csv",stringsAsFactors=F)

BoxplotTtest <- function(dataset,gene_name){
  data <- subset(dataset,gene==gene_name,)
  Pvalue <- t.test(dCt ~ condition,data)$p.value
  boxplot(FOLD~condition,data,main=gene_name)
  return(Pvalue)
}
genes <- unique(pcr_data$gene)
par(mfrow=c(2,2))
sapply(genes,function(x) {BoxplotTtest(pcr_data,x)})

##      IL12      IL1B     CXCL2       TNF 
## 0.6610609 0.7385934 0.6402007 0.6737587