R help - Jun 2017 - DESeq2 pairwise compasion

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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I think you are asking on the wrong mailing list. Perhaps you should be asking
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-- 
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On June 8, 2017 7:35:55 AM PDT, Yogesh Gupta <yogesh2cute at gmail.com>
wrote:
>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