2021-04-16 用limma包做差异分析

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# 用limma包做差异表达分析
#差异分析重点在于做好表达矩阵和分组信息，具体原理可以不用理解
suppressMessages(library(limma)) 
design <- model.matrix(~0+factor(group_list))
colnames(design)=levels(factor(group_list))
rownames(design)=colnames(exprSet)
design
contrast.matrix<-makeContrasts(paste0(unique(group_list),collapse = "-"),levels = design)
contrast.matrix 
##step1
fit <- lmFit(exprSet,design)
##step2
fit2 <- contrasts.fit(fit, contrast.matrix) ##这一步很重要，大家可以自行看看效果
fit2 <- eBayes(fit2)  ## default no trend !!!
##eBayes() with trend=TRUE
##step3
tempOutput = topTable(fit2, coef=1, n=Inf)
nrDEG = na.omit(tempOutput) 
#write.csv(nrDEG2,"limma_notrend.results.csv",quote = F)
head(nrDEG)
参考：https://www.jianshu.com/p/1537efae5be9
http://www.bio-info-trainee.com/bioconductor_China/software/limma.html