Question: DESeq2 statistic and design
gravatar for Merlin
8 days ago by
Merlin 10
Merlin 10 wrote:

Hello everyone, I am using DESeq2 for DEG analysis. I have a set of experiment which consists of 4 duplicates and it's not clear how to create the design object?

Here is my condition:

condition<- factor(c (group1 =rep ("treatment1",time=2), group2 = rep("treatment2",time=2), group3= rep("treatment3",time=2),group4 =rep("treatment4",time=2)))


 dds <- DESeqDataSetFromMatrix(countdata, coldata, design=~condition )

I think I should normalize within each group and compare the DE among groups.

Also, I’m a bit confused about what statistic method to apply with DESeq, contrast or interaction?

Thank you for help

deseq2 rna • 74 views
ADD COMMENTlink modified 8 days ago by Michael Love23k • written 8 days ago by Merlin 10
Answer: DESeq2 statistic and design
gravatar for Michael Love
8 days ago by
Michael Love23k
United States
Michael Love23k wrote:

Take a look at the vignette and the help page for ?results.

You can compare any groups using “contrast” in results and we have examples.

ADD COMMENTlink written 8 days ago by Michael Love23k
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