Limma-voom can't find object

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1

Hey guys,

First time posting here. I’m running an RNA-seq analysis but I am stuck at the Limma-voom step.

Here’s the error I am getting:
Error in eval(ej, envir = levelsenv) : object ‘Control_Old’ not found
Calls: makeContrasts → eval → eval
Execution halted

I just genuinely can’t understand how it isn’t found. I double checked the spelling and everything.

2

Hi, did you ever work out the solution to this problem? I’m having the same issue.

Thanks!

3

Hi @EmWhat

This error comes up when the tool cannot build a data structure properly during processing. This is an R error, so R formatting requirements need to be met.

The tool form has examples/detailed help for each of these:

  1. At least two groups are input
  2. Each group contains at least two count inputs
  3. The same number of count files were input per group
  4. Labels for groups are all “oneword” or “one_word”. Alphanumeric characters plus (optionally) underscores.
  5. If you are inputting a matrix instead of individual count files, the same labeling rules would apply.
  6. Same for contrast inputs – full group labels separated by a dash “-”.
  7. Whitespace or any other characters will cause interpretation problems.

If you can’t find the problem, please post back either a shared history link or a screenshot of the job details page for one of the errored outputs (specifically, the portion of the log where the tool version and inputs/parameters are listed out). How to do both is explained here troubleshooting-errors

Let’s start there :slight_smile:

Related prior Q&A: edgeR error in galaxy