EdgeR Tutorial for Differential Gene Expression

[Avantika_Bansal]

I wanted to use EdgeR for DEG but couldn’t find the tutorial. I have used DESeq2 previously but it was giving errors as I have only one sample for each control and treated. So I wanted to use EdgeR. Is there any tutorial of this tool like we have for DESeq2?
I’ll be highly thankful.

[jennaj]

Hi @Avantika_Bansal

All of the Bioconductor tools require replicates as far as I know. And they definitely do for the wrapped version of tools hosted in Galaxy.

Cross Reference

@jennaj

Replicates will be required to use this tool and the other Bioconductor DE tools.

FAQ Extended Help for Differential Expression Analysis Tools

And, here is a summary from another person on our team, who captures the situation well, so am just quoting.

Yes, that is the problem.

See also DESeq2 without biol replicates - SEQanswers where Simon Anders and Michael Love chime in, the original authors of DESeq and DESeq2.

I think the best you can do is to normalize the counts and look at the fold changes, but none of that is really statistically sound.

Usage help is at the very bottom of the tool forms. It is too much for this tool to quote and post back, but if you search the tool panel for the tool, click into it, then scroll down you’ll find it.

For example data, the tutorial data associated with Limma and DESeq2 should also work fine for EdgeR. Find links to available tutorials also at the bottom of tool forms. Not every tool has a Galaxy tutorial, but if anything is known about external resources, that is also linked onto the tool forms.

If you run into a usage problem that you can’t solve, you can ask more about it here and we can try to help.

[Avantika_Bansal]

Thanks for the explanation. I’ll go through it.