List with zero data sets in Limma voom

Welcome, @shrutikane

Thanks for the great screenshot, very helpful!

Not including count replicates is what I can see as at least one problem right now.

If you opened up the Tool Standard Error (stderr) it will probably report that the tool is expecting “replicates” and didn’t find them (unless some other problem was encountered first!).

In practical use, this means two or more Factor levels with two or more count files each. So, a minimum of one Factor, two Factor levels, four Sample count files for a simple run. All of the differential expression tools written by Bioconductor require replicates.

We have some help about this and other common usage help in a GTN guide here → FAQ: Extended Help for Differential Expression Analysis Tools.

Quote from that guide

  • Differential expression tools all require sample count replicates. Rationale from two of the DEseq tool authors.
    • At least two factor levels/groups/conditions with two samples each.
    • All must all contain unique content for valid scientific results.

For definitive help, please refer to the tool vignette and publications (linked at the bottom of the Galaxy tool form), plus see our Limma Tutorials for more Galaxy examples, including sample data, methods, and a workflow template.

In short: usage is about the same between all platforms (R or Galaxy or a Notebook of any kind) since the underlying tool is the same everywhere… and we can help with the “translate to a Galaxy tool form” parts here at this forum.

It looks like you are following a tutorial of some sort but I don’t recognize it. You can refer the instructor to this post, and you or they are welcome to ask more questions. Please include a link to the tutorial as a reference, along with a shared history link (with at least the starting data run through upstream steps) if at all possible.

Hope this helps! :slight_smile:

Xref EdgeR Tutorial for Differential Gene Expression - #2 by jennaj