[BioC] DESeq2(analysis without replicate)

Hui Zhao [guest] guest at bioconductor.org
Mon Dec 9 04:41:39 CET 2013


I want to know how to deal with data without replicates using DESeq2,can you tell me how to deal with it.You can see my codes below,but it have errors when deal with sample without replicates.

 -- output of sessionInfo(): 

     library('DESeq2')
     readcount<-read.delim("readcount.xls",row.names=1)
     readcount<-round(readcount)
     readcount<-readcount[,c(1,3)]
     colData<-data.frame(condition=c("A","B"))
     row.names(colData)<-c("A","B")
     colData
     dds<-DESeqDataSetFromMatrix(countData=readcount,colData=colData,design=~condition)
     colData(dds)$condition<-factor(colData(dds)$condition,levels=c("A","B"))
     dds <- DESeq(dds)
     res<-results(dds)
     res<-res[order(res$padj),]
     res<-as.data.frame(res)
 

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