R语言 在做基因差异表达时下标出界

library(Biobase)

library(BiocGenerics)

library(affy)

library(limma)

library(pheatmap)

filename = list.files("CCLEpaxOVrna") 

dir = paste("./CCLEpaxOVrna/",filename,sep="") 

n = length(dir)

data = ReadAffy(filenames=filename[1] )

for (i in 2:n){ new.data = ReadAffy(filenames = filename[i])

data = merge(data,new.data)}

aaa<-rma(data)

aa2<-exprs(aaa)

head(aa2)

control<-aa2[,c(5,6,10,20)]

LPS<-aa2[,-c(5,6,10,20)]

design <- model.matrix(~ -1+factor(c(1,1,1,1, 2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2)))

colnames(design) <- c("control", "LPS")

fit <- lmFit(aa2, design)

contrast.matrix <- makeContrasts(control-LPS, levels=design)

fit <- eBayes(fit)

fit2 <- contrasts.fit(fit, contrast.matrix)

fit2 <- eBayes(fit2)

dif<-topTable(fit2,coef="control-LPS",n=nrow(fit2),lfc=2)

dif<-dif[dif[,"P.Value"]<0.5

head(dif)

> dif<-topTable(fit2,coef="control-LPS",n=nrow(fit2),lfc=2)

Error in fit$coefficients[, coef] : 下标出界