[R] DESeq2 pairwise compasion

Yogesh Gupta yogesh2cute at gmail.com
Thu Jun 8 16:35:55 CEST 2017

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


countMatrix = read.table("read_count.22May.2017.new.txt",header=T,sep='\t',check.names=F)


[1] 57894    35

Now I am not sure how to construct a DESeqDataSet:

dds <- DESeqDataSetFromMatrix(countData = countMatrix,

colData = colData,

design = ~ condition)



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

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