Tool Error interpretation

input
error
deseq2
edger
limma
#1

What does this error mean?

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

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#2

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.

#3

Thank you for your response.
1- The name and version of the tool is DESeq2
2- (Galaxy Version 2.11.40.2)- I am running it through usegalaxy.org (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.

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#4

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.

Options:

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: https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html

Note: At this time, that tutorial still under development. Once the tutorial finalized, it will be listed here: https://galaxyproject.github.io/training-material/topics/transcriptomics/. 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 https://usegalaxy.org server yet – but I’m fairly certain the tools are at Galaxy EU https://usegalaxy.eu server (the server used for development of the tutorial) – and if not for some reason, that could be part of your feedback.

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