logFoldChange=1>
adjustP=0.05>
> library(limma)>
setwd("C:\\Users\\仁爽\\Desktop\\新建檔案夾 (3)\\07.diff")> rt=read.table("normalize.txt",sep="\t",header=T,check.names=F)>
rt=as.matrix(rt)> rownames(rt)=rt[,1]> exp=rt[,2:ncol(rt)]> dimnames=list(rownames(exp),colnames(exp))>
rt=matrix(as.numeric(as.matrix(exp)),nrow=nrow(exp),dimnames=dimnames)>
>differential> modType=c(rep("normal",8),rep("tumor",40),rep("normal",6),rep("tumor",17),rep("normal",15),rep("tumor",31))
> design <- model.matrix(~0+factor(modType))> colnames(design) <- c("con","treat")> fit <- lmFit(rt,design)> cont.matrix<-makeContrasts(treat-con,levels=design)
> fit2 <- contrasts.fit(fit, cont.matrix)> fit2 <- eBayes(fit2)> > allDiff=topTable(fit2,adjust='fdr',number=200000)> write.table(allDiff,file="limmaTab.xls",sep="\t",quote=F,row.names=F)> > #write table> diffSig <- allDiff[with(allDiff, (abs(logFC)>logFoldChange & adj.P.Val < adjustP )), ]> write.table(diffSig,file="diff.xls",sep="\t",quote=F,row.names=F)
> diffUp <- allDiff[with(allDiff, (logFC>logFoldChange & adj.P.Val < adjustP )), ]
>write.table(diffUp,file="up.xls",sep="\t",quote=F,row.names=F)> diffDown <- allDiff[with(allDiff, (logFC<(-logFoldChange) & adj.P.Val < adjustP )),
> write.table(diffDown,file="down.xls",sep="\t",quote=F,row.names=F)>
> #write expression level of diff gene> hmExp=rt[as.vector(diffSig[,1]),]
Error in rt[as.vector(diffSig[, 1]), ] : 下標出界> diffExp=rbind(id=colnames(hmExp),hmExp)
Error in is.data.frame(x) : 找不到物件'hmExp'> write.table(diffExp,file="diffExp.txt",sep="\t",quote=F,col.names=F)
Error in is.data.frame(x) : 找不到物件'diffExp'
是什么原因？要如何補救呢？謝謝大神們
uj5u.com熱心網友回復：
檢查一下你合并前的檔案，是不是有的表達值已經取了log，有的沒有，導致去除批次效應后檔案有誤。uj5u.com熱心網友回復：
樓主，這個問題有解決嘛轉載請註明出處，本文鏈接：https://www.uj5u.com/qita/16558.html
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