I am working on DEseQ2 to find the differentially expressed when i compare the control (3 replicates) Vs. 2 treated samples (3 replicates each, and 6 in total for treated condition) . I am mainly interested in the genes those are differentially expressed when i compare the two treatments to the control.
But im not sure how to set up an experiment in Deseq2
control1 s1 control
control2 s2 control
control3 s3 control
Ec32.Eury05.T1 s4 Sus
Ec32.Eury05.T2 s5 Sus
Ec32.Eury05.T3 s6 Sus
Ec32.Eury96.T1 s7 Sus1
Ec32.Eury96.T2 s8 Sus1
Ec32.Eury96.T3 s9 Sus1
So far the commands i used were
coldata<-data.frame(row.names=colnames(Sum_rep.df),cell=paste0("s", 1:9), dex= c(rep('control', 3), rep('Sus',3), rep('Sus1',3)))
dds <- DESeqDataSetFromMatrix(countData = round(Sum_rep.df), colData = coldata, design = ~ dex)
Could someone direct me , if its right?
Any help would be appreciated