贝叶斯t-test

setwd("E:/TCGA-mRNA/new/merged_tpm/")

data<-read.table("COAD.sort.rpkm.txt",head=T,sep="\t",row.names=1)

source("d:/desktop/bayesreg.R")

library(multtest)

T<-bayesT(data,numC= ,numE= ,ppde=TRUE,betaFit=1,bayes=TRUE,doMulttest=1)

write.table(T,"bayes",quote=F,col.names=TRUE,sep="\t"))

limma

library(edgeR)

library(limma)

lncRNA<-read.table("D:/Desktop/BRCA/RNAseq/filter_lncRNA.txt",header = TRUE,sep = "\t",row.names = 1)

group<-factor(c(rep("C",113),rep("E",1109)))

genelist <- DGEList(counts = lncRNA,group = group)

keep <- rowSums(cpm(genelist)>0.5)>=2

genelist.filted <- genelist[keep,,keep.lib.sizes=FALSE]

x <- calcNormFactors(genelist.filted,method = "TMM")

design<-model.matrix(~0+group)

colnames(design)<-c("C","E")

logCPM <- cpm(x,log = TRUE,prior.count = 3)

fit<- lmFit(logCPM,design)

cont.matrix=makeContrasts("C-E",levels = design)

fit2=contrasts.fit(fit,cont.matrix)

fit<-eBayes(fit2,trend = TRUE)

res<-topTable(fit,number = nrow(lncRNA))

write.table(res,"D:/Desktop/BRCA/RNAseq/DEG_lncRNA.txt",quote = FALSE,sep = "\t")