Question: DESeq2 analysis without Replicate
0
gravatar for Sushant Pawar
3.5 years ago by
Nashik
Sushant Pawar0 wrote:

Hi all ,

I am new to this field of Transcriptome analysis , so please help me in this.

         I just want to know that can we run DESeq2 for without replicate of treated and Untreated .If yes then what should the change in the syntax of DESeq2 .Below is the syntax i am using for with Replicate samples.

And if no , then what is the other tool should i use for this type of analysis.

====================================================================================

library(DESeq2)
library(DESeq2)
directory<-"/home/dgl/projects/110_AmpliseqRNA/all_samples_with-replicates/Cervical-Liver"
sampleFiles <- grep("treated",list.files(directory),value=TRUE)
sampleCondition<-c("treated","treated","treated","untreated","untreated","untreated")
sampleTable<-data.frame(sampleName=sampleFiles, fileName=sampleFiles, condition=sampleCondition)
sampleTable
ddsHTSeq<-DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=directory, design=~condition)
colData(ddsHTSeq)$condition<-factor(colData(ddsHTSeq)$condition, levels=c("untreated","treated"))
dds<-DESeq(ddsHTSeq,fitType="mean")
res<-results(dds)
res<-res[order(res$padj),]
head(res)

mcols(res,use.names=TRUE)
write.csv(as.data.frame(res),file="Raw_File_deseq2.csv")

FileforIpathway=res[,c(2,6)]
write.csv(as.data.frame(FileforIpathway),file="File_for_iPathway_deseq2.csv")

pdf("DEseq2_MA_plot.pdf")
plotMA(dds,ylim=c(-10,10),main="DESeq2")
dev.off()

pdf("DESeq2_Dispersion_plot.pdf")
plotDispEsts(dds)
dev.off()

==========================================================================================

deseq2 without replicate • 2.1k views
ADD COMMENTlink modified 3.5 years ago by Michael Love24k • written 3.5 years ago by Sushant Pawar0
Answer: DESeq2 analysis without Replicate
0
gravatar for Michael Love
3.5 years ago by
Michael Love24k
United States
Michael Love24k wrote:
There's no change to the syntax. You just run DESeq() and it detects there are no replicates. It should direct you to read a section of ?DESeq for more information.
ADD COMMENTlink written 3.5 years ago by Michael Love24k
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