DESEq2 error while running

I am facing this error while performing differential gene expression. My dataset has Ensemble id and corresponding to it is gene expression count. Please help me to resolve the error.

Hi @Avantika_Bansal

We’ll need more details to help. Please consider Sharing your History or posting content from the Job Information :information_source: view as described in Troubleshooting errors.


Sure. I will provide the details. I have this error whenever I use limma. I have annotated my files with respect to ensemble but I am still facing the same issue.

Hi @Avantika_Bansal

Thanks for sharing.

The important part of the error message is this:

more columns than column names

It is a message directly from the underlying tool. And means that the tool was trying to create a table of data and it didn’t find a header for all of those columns. That problem could be with the count files (one or more) or the reference file.

This prior Q&A was about a similar issue: DEseq2 Error in read.table

Examples of what those files should contain is at the bottom of the tool form in the help sections, and more examples are in this tutorial 2: RNA-seq counts to genes

Try comparing your data versus those examples. If you need more help, please post back a screenshot of the section right above the one you posted (Tool Parameters). Be sure to click on the input files to expand them please, to show the first few lines in the “peek” view.

Thank you, I will do that.