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Question: DESeq2(analysis without replicate)
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4.0 years ago by
Guest User12k
Guest User12k wrote:
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,d esign=~condition) colData(dds)$condition<-factor(colData(dds)$condition,levels=c("A ","B")) dds <- DESeq(dds) res<-results(dds) res<-res[order(res$padj),] res<-as.data.frame(res) -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 4.0 years ago by Michael Love15k • written 4.0 years ago by Guest User12k
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gravatar for Michael Love
4.0 years ago by
Michael Love15k
United States
Michael Love15k wrote:
hi Hui Zhao, This code looks correct for the exploratory analysis without replicates. Can you explain and paste the content of the errors you are experiencing? It looks like you are rounding the values of the readcount object. Note that our software is designed to work on raw, unnormalized counts of reads in features. Mike On Sun, Dec 8, 2013 at 10:41 PM, Hui Zhao [guest] <guest@bioconductor.org>wrote: > > I want to know how to deal with data without replicates using DESeq2,can > you tell me how to deal with it.You can see my codes below,but it have > errors when deal with sample without replicates. > > -- output of sessionInfo(): > > library('DESeq2') > readcount<-read.delim("readcount.xls",row.names=1) > readcount<-round(readcount) > readcount<-readcount[,c(1,3)] > colData<-data.frame(condition=c("A","B")) > row.names(colData)<-c("A","B") > colData > > dds<-DESeqDataSetFromMatrix(countData=readcount,colData=colData,des ign=~condition) > > colData(dds)$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) > > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
ADD COMMENTlink written 4.0 years ago by Michael Love15k
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