How should I prepare the correct input file to run CEMiTool without bug?

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1

I am trying to perform gene co-expression analysis using CEMiTool. My input file is in TSV format where the first column contains gene IDs and all subsequent columns contain expression data like attaching screenshot.

However, when I run CEMiTool with my input data, I continuously receive a bug report. I’ve tried various modifications, but I still get the same error. How can I determine what’s wrong with my file and fix this bug? Also, I attached the bug-report below. What does this bug report mean, and what should I change?

  • my input data

image
image422×297 17.9 KB

  • bug-report

675745
6757451418×942 78.2 KB

2

Welcome @ohoh

We have a prior topic here where we covered the usage. → How to tell the CEMiTool that the input file is an expression matrix? It treats gene names as part of the matrix and gives an error that it only accepts numeric data

For what I can see in your data, removing the “gene_id” header might be enough. But you might also need to replace the dot “.” characters in the first column’s values (replace with an underscore “_” or simply remove them.

In short, make everything R friendly, then follow the expected formatting assumptions by this specific tool too.

You can make the changes either in Galaxy using text manipulation tools or make the changes before loading the data up to Galaxy.

Please give that a try and let us know how it works! :slight_smile: