There are two line 216 and 218
Three development stages 5 WEEK (5W), 7W, 9W.
Three tissue: Ca, Co, Pa
each with 2 biological replicate.
With two biological replicate. I want to do differential gene expression analysis using DESeq2 so I tried these codes after reading about DESeq2: ,my aim is to do the pairwise comparison. how to make colData and design formula.
library("DESeq2")
countMatrix = read.table("read_count.22May.2017.new.txt",header=T,sep='\t',check.names=F)
head(countMatrix)
dim(countMatrix)
[1] 57894 35
Now I am not sure how to construct a DESeqDataSet:
dds <- DESeqDataSetFromMatrix(countData = countMatrix,
colData = colData,
design = ~ condition)