Question: Differential Gene expression analysis with two factors
0
gravatar for mahnazkiani
19 months ago by
mahnazkiani40
United States
mahnazkiani40 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 • 612 views
ADD COMMENTlink modified 19 months ago by Devon Ryan89k • written 19 months ago by mahnazkiani40

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 19 months ago by mahnazkiani40

That would be undesirable when there are known better methods.

ADD REPLYlink written 19 months ago by Devon Ryan89k
1
gravatar for Devon Ryan
19 months ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k 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 19 months ago by Devon Ryan89k
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