Pvalue Compare Between LUAD and LUSC based on paired samples

In order to check the difference of the P-values with paired and non-paired samples, as well as between LUSC and LUAD. We conducted the following analysis.

first we should load our customed R function for t-test or wilcox test

 library("stringr")
  PairWilPValue<-function(data,x1,x2){
    output<-matrix(NA,dim(data)[1],5)   # set output matrix ()
    for(i in 1:dim(data)[1]){
      out<-data.frame()
      if(all(! any(all(is.na(data[i,x1])),all(is.na(data[i,x2]))),sum(is.na(data[i,]))<0.5*length(data[i,]))){ 
        tmp1<-try(wilcox.test(as.numeric(data[i,x1]),as.numeric(data[i,x2]),paired=T, na.action=na.omit))
        output[i,1]<-tmp1$p.value
        output[i,2]<-mean(as.numeric(data[i,x1]))-mean(as.numeric(data[i,x2]))
        output[i,3]<-"wilcox"
        output[i,4]<-mean(as.numeric(data[i,x1]))
        output[i,5]<-mean(as.numeric(data[i,x2]))
        #      print(i)
      }
    }
    out<-cbind(rownames(data),output)
    out
  }
  
  PairttestPValue<-function(data,x1,x2){
    output<-matrix(NA,dim(data)[1],5)   # set output matrix ()
    for(i in 1:dim(data)[1]){
      out<-data.frame()
      if(all(! any(all(is.na(data[i,x1])),all(is.na(data[i,x2]))),sum(is.na(data[i,]))<0.5*length(data[i,]))){ 
        tmp1<-try(t.test(as.numeric(data[i,x1]),as.numeric(data[i,x2]),paired=T, na.action=na.omit))
        output[i,1]<-tmp1$p.value
        output[i,2]<-mean(as.numeric(data[i,x1]))-mean(as.numeric(data[i,x2]))
        output[i,3]<-"wilcox"
        output[i,4]<-mean(as.numeric(data[i,x1]))
        output[i,5]<-mean(as.numeric(data[i,x2]))
        #      print(i)
      }
    }
    out<-cbind(rownames(data),output)
    out
  }
  
  NonPairttestPValue<-function(data,x1,x2){
    output<-matrix(NA,dim(data)[1],5)   # set output matrix ()
    for(i in 1:dim(data)[1]){
      out<-data.frame()
      if(all(! any(all(is.na(data[i,x1])),all(is.na(data[i,x2]))),sum(is.na(data[i,]))<0.5*length(data[i,]))){ 
        tmp1<-try(t.test(as.numeric(data[i,x1]),as.numeric(data[i,x2]),paired=F, na.action=na.omit))
        output[i,1]<-tmp1$p.value
        output[i,2]<-mean(as.numeric(data[i,x1]))-mean(as.numeric(data[i,x2]))
        output[i,3]<-"wilcox"
        output[i,4]<-mean(as.numeric(data[i,x1]))
        output[i,5]<-mean(as.numeric(data[i,x2]))
        print(i)
      }
    }
    out<-cbind(rownames(data),output)
    out
  }

1. P-value between LUSC and LUAD based on paired samples

setwd("/home/sguo/Dropbox/Project/PanCancer/Rmd")
load("luad.pair.pvalue.RData")
load("lusc.pair.pvalue.RData")
P11<-log(as.numeric(P1),10)
P12<-log(as.numeric(P2),10)
plot(P11,P12,cex=0.4,xlab="Lung adenocarcinoma",ylab="Lung Squamous Cell Carcinoma")
abline(v=log(0.05/length(P11),10),lty=2,col=2,lwd=2)
abline(h=log(0.05/length(P11),10),lty=2,col=3,lwd=2)

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