DESeq2 design formula/experiment table help
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@greenhawmatt-12843
Last seen 7.0 years ago

Hi,

I am following a DESeq2 tutorial (see link below) and I have a question about setting up the experiment table and design formula. 

https://www.bioconductor.org/help/course-materials/2015/LearnBioconductorFeb2015/B02.1.1_RNASeqLab.html

The data that I have is made up of 3 groups (control, knockout_a, knockout_ab), and each group has 4 replicates. 

Here is the experiment design table that I created:

  run knockout
control_replicate_1 control_replicate1 control
control_replicate_2 control_replicate2 control
control_replicate_3 control_replicate3 control
control_replicate_4 control_replicate4 control
a_replicate1 a_replicate1 a
a_replicate2 a_replicate2 a
a_replicate3 a_replicate3 a
a_replicate4 a_replicate4 a
ab_replicate1 ab_replicate1 ab
ab_replicate2 ab_replicate2 ab
ab_replicate3 ab_replicate3 ab
ab_replicate4 ab_replicate4 ab

 

I am trying to find find the differential expression of:

control vs knockout_a

control vs knockout_ab

knockout_a vs knockout_ab 

I would also like retain the ability do PCA for all 3 groups (1 plot) and for each comparison group (3 plots).

When I run  ( dds <- DESeqDataSet(se, design = ~ knockout) ) I believe it just compares "control vs ab". 

Is there a way to modify the design table and/or design formula to express what I am trying to do? Or will I have to create 3 separate design tables (for each of the 3 comparisons) to achieve my goal? Along with that, any clear explanation for how the design table and design formula are connected would be much appreciated.

 

Thanks for your help!

rnaseq differential gene expression deseq2 r • 1.6k views
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Entering edit mode
@mikelove
Last seen 1 hour ago
United States

Have you taken a look at the vignette:

vignette("DESeq2")

Also it's described in

?results

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