Tool Error interpretation



What does this error mean?

ncol(countData) == nrow(colData) is not TRUE


This probably indicates a usage or data input problem with a tool.

Technically, this is reporting that the number of expected columns is not matching the number of rows in some calculation – but that is not enough to offer actionable help.

Please reply back with a bit more information:

1 - What is the name and version of the tool are you using? Click on the rerun button and copy the name/version of the tool back in the reply.

2 - Where are you running the tool? If a public server, capture the base URL. If your own Galaxy, what version was installed?

Let’s start there. We might recognize the problem/usage issue and be able to offer help, or this will guide us about what other information is needed to diagnose/offer troubleshooting help.


Thank you for your response.
1- The name and version of the tool is DESeq2
2- (Galaxy Version I am running it through (so I guess I am running it on a cloud server?)
More info: the first column of my data is gene name and the rest of the columns are count data. I am thinking the issue might have something to do with the first column.


Hi - Thanks for the extra information!

The problem is with the format of the count input datasets. Each sample needs to be run through a supported count tool and entered individually under Factor/Factor levels. Details are on the DEseq2 tool form.

Since your data has the counts in a matrix, that won’t work with DEseq2 as currently wrapped for Galaxy.


To use DESeq2, I would suggest generating the counts within Galaxy. Or, you could run one of your samples in Galaxy, compare those results to your per-sample counts generated outside of Galaxy (individual counts, before merged into a matrix), and make changes to sync up the formatting as needed.

Consider alternative tools. Limma/EdgeR do support count matrix input. How to use each is described on their tools forms with example data input content/format.

Limma DE (with matrix input) is included in this provisional Galaxy Training Network (GTN) Tutorial:

Note: At this time, that tutorial still under development. Once the tutorial finalized, it will be listed here: Feedback to the GTN about it would be welcomed to help us improve it – find the feedback form at the end of the tutorial. If you want to use all the tools in the tutorial, those might not be all at Galaxy Main server yet – but I’m fairly certain the tools are at Galaxy EU server (the server used for development of the tutorial) – and if not for some reason, that could be part of your feedback.