Paired samples in DESeq2
1
0
Entering edit mode
m.wekking • 0
@mwekking-19794
Last seen 5.1 years ago

So I am no R programmer and my skills in this languages are very limited but I needed to perform a certain analysis in it. I needed to use DESeq2, after many hours I finally got a working script.

library(DESeq2)
a = read.table (file = "superEnhancer_counts.txt",header = T,sep = "\t",row.names = 1)

coldata = read.table(file = "superEnhancer_names.txt",header = T,sep = "\t")[,] 
dso = DESeqDataSetFromMatrix(countData = a,colData = coldata,design =  ~ Sample)
dsoA<-DESeq(dso )
write.table((results(dsoA)),file="results.txt",sep = "\t",quote = F)
dev.off()

not the prettiest but it works ... But now I need to perform a DESeq2 analysis with paired samples. So two samples are from the same patients. I have read many posts about this but for the world can't figure it out .. is there anybody that can help? This is the name.txt file:

Name    Sample
a_unst1 a_unst
b_Rux1  b_Rux
b_Rux2  b_Rux
a_unst2 a_unst
b_Rux3  b_Rux
a_unst3 a_unst
b_Rux4  b_Rux
a_unst4 a_unst

So the unst1 should be paired with the Rux1, the unst2 with the rux2 etc...

R deseq2 Paired Samples • 625 views
ADD COMMENT

Login before adding your answer.

Traffic: 641 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6