edgeR Error Message

I received the following error message while running edgeR, please address this issue, thanks!

Warning message:
In Sys.setlocale(“LC_MESSAGES”, “en_US.UTF-8”) :
OS reports request to set locale to “en_US.UTF-8” cannot be honored
Error in glmFit.default(sely, design, offset = seloffset, dispersion = 0.05, :
nrow(design) disagrees with ncol(y)
Calls: estimateDisp … estimateDisp → estimateDisp.default → glmFit → glmFit.default

Hi @lordyiffles

I replied to your bug report already but for others reading:

This type of error message from any Bioconductor or R tool means that there is a labeling problem or design problem. The details usually have some clues – this message is stating that the tool ran into a mismatch between the rows and columns of the inputs.

Click into the :information_source: icon for a dataset to see what was used to produce that data (error or success). This is an easier view to review tool inputs and parameters in a summary format. Often, this alone reveals what the job problems were, along with the content of the logs on that same view (stderr, stdout). And, this is the same information to share when asking a question here.

For your data, it looks like there is an extra column in the count matrix that is not associated with a sample name in the factor matrix. The tool Cut can be used to remove that column.

Examples of these data are on the tool form, plus at the resources below. You might also need to:

  1. adjust headers in the factor matrix
  2. remove Geneid rows from the count matrix if all sample counts are 0
  3. find out why the “database” metadata is set to hg38Patch11 instead of just hg38 for both of these inputs. Only hg38 is indexed at the usegalaxy.* servers. Avoid assigning native metadata keys unless you are certain they apply. Mixups can lead to content problems that are very hard to detect.


Galaxy Tutorials

Related Q&A at this Galaxy Forum

Other Forums – many existing public solutions will also apply to the Galaxy wrapped versions of tools. Searching with error codes is usually enough. If you can’t find a solution, or need help translating a command-line function to a Galaxy tool form’s options, please come back and ask your question here.

Thanks! :rocket: