Question: Differential Gene expression analysis with two factors
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gravatar for mahnazkiani
2.1 years ago by
mahnazkiani50
United States
mahnazkiani50 wrote:

Hi,

I have a question about RNA-seq data analysis, I have two genotypes and 3 sampling from a different part of the plant in each genotype. I want to analyze both genotypes together using factor analysis with a genotype: stage interaction term. How I can do that? Can I use edgeR?

Appreciate your help, Mahnaz

rna-seq • 707 views
ADD COMMENTlink modified 2.1 years ago by Devon Ryan91k • written 2.1 years ago by mahnazkiani50

Just wondering that does it makes sense to get DEGs from two genotypes and then use venn diagram to find similar DEGs in two genotypes and go through functional analysis after that?

ADD REPLYlink written 2.1 years ago by mahnazkiani50

That would be undesirable when there are known better methods.

ADD REPLYlink written 2.1 years ago by Devon Ryan91k
1
gravatar for Devon Ryan
2.1 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

Yes, you can certainly do that with edgeR (or DESeq2 or limma). If you really want the interaction term then use a model of ~genotype*stage and get the adjusted p-values/fold-changes for the interaction. Have a look at section 3.3 in the edgeR user guide for designs including interactions.

ADD COMMENTlink written 2.1 years ago by Devon Ryan91k
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