Need help explain Heinz tutorial and help with workflow

1

Hi everyone
I having some trouble with this tutorial for heinz
tutorial:

Can someone explain the figure

Heinz_visualisation
Heinz_visualisation860×1414 92.8 KB

that is: Visualize
the output: visualize the optimal subnetwork. It’s
where you have the circles,lines, and the
numbers that are in the circles. Don’t understand
what the numbers mean
Also, my workflow chart keeps getting errors

2

Hi @Rahul_Nadkarni

Each box has four values. The first two are the ones to pay attention to for the exercise.

  1. The first value is the “K0” identifier – this is a Gene identifier from KEGG Ontology
  2. The second value is the Heinz score. It is calculated using the data from the input file generated in upstream steps.

From the tutorial

Comment: What is the Heinz score?

To figure out this score without reading the formula, we can understand Heinz score in this way. FDR is involved in calculating a p-value threshold and any KO whose p-value is below this threshold is regarded as significant, which means the Heinz score is positive (another calculation in the formula). If we pick a higher FDR value, then we will have a higher p-value threshold, and more KOs are probably regarded as significant. In this situation, we probably have many false positive (those regarded as significant are actually not) on the one hand; on the other hand, Heinz will deliver a bigger subnetwork, which might be exhausting to analyze. Therefore, we need to pick up an FDR value properly.

And

Question
According to the figure above, Why are some shapes are round, others square?

Solution
Round shape corresponds to positive Heinz score; square shape corresponds to negative Heinz score.

  1. I’m not sure what the third and fourth values represent. It seems the tutorial author (!) had the same question for the tool author → Understand the output of Heinz · Issue #15 · ls-cwi/heinz · GitHub.

The tutorial lists out alternative ways to do the graphing that might clarify some of this. As suggested, you could also try using different FDR thresholds with the upstream tools to see what results.

For this part:

I ran a test history to make sure the workflow was functioning at UseGalaxy.org correctly. The tools have been updated which is why you’ll see warnings after importing. Don’t attempt to run a workflow that is presenting with warnings. Instead, open it up the workflow in the editor, and review.

For this one, open it then save, then run it. This addresses these specific warnings to update the tools to the current versions the UseGalaxy.org server happens to hosts. If you imported on different servers, the warnings might be different.

Note: None of the current warnings at UseGalaxy.org lead to meaningful changes except for the tool version updates, and that is automatic with the “open in editor and save”. That won’t always be true, even when using workflows from tutorials. If you have a question about some other workflow in the future that does require changes beyond this (some non-automatic change), feel free to ask a question if the warning description is not enough to solve the issue.

Hope this helps! :slight_smile:

Ping @zhang123, this was your tutorial, correct? Would you like to comment more?