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)
Thanks
Yogesh
--
*Yogesh Gupta*
*Postdoctoral Researcher*
*Department of Biological Science*
*Seoul National University*
*Seoul, South Korea*
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