DESeq2 pairwise compasion

2 messages · Yogesh Gupta, Jeff Newmiller

Thu, Jun 8, 2017 7:35 AM #

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*

	[[alternative HTML version deleted]]

Jeff Newmiller

Thu, Jun 8, 2017 9:32 AM #

I think you are asking on the wrong mailing list. Perhaps you should be asking this question on the Bioconductor mailing list?

Sent from my phone. Please excuse my brevity.

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