Error running edgeR

usegalaxy.org support
, ,
1

Hi,

I am having trouble getting edgeR to run on my featureCounts files. I am trying to feed in 2 conditions (day 6 and day 9 samples), with 3 replicates each. However, I get an error saying:
" 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 [<-.data.frame(*tmp*, files, factorname, value = “day_9”) :
column name “” cannot match any column
Calls: [<- → [<-.data.frame"

This comes with a suggestion:
“Detected Common Potential Problems
The tool was started with one or more duplicate input datasets. This frequently results in tool errors due to problematic input choices.”

The error and suggestion point at column names being the issue or duplicate datasets. I have tried renaming the columns in the 6 files I have and reran the analysis, to no avail. I also made sure the files actually contain unique data, and are not accidentally copies of the same dataset with a different name. Still, the tool returns the error.

Please find included my history: Galaxy
Sorry it is a bit of a mess, I tried to rerun the same analysis several times as described above.

If anyone could point me to where my issue might lie, I would greatly appreciate it!

Cheers,
Wouter

2

Hi @Thoughtfather

I’m reviewing. Thanks for posting the history link, super helpful! :slight_smile:

3

Well, that was fast! The factor “Name” value was left empty, and while that is technically optional, I started up a rerun to see if adding that in would be enough.

Ok, that completed quickly, and it was enough. I’ll ticket that and post the issue link back here sometime today. Update → Bug fix: missing (optional) factor or group name results in unclear error with EdgeR · Issue #6297 · galaxyproject/tools-iuc · GitHub

Test history (copy of your with the extra run). I can unshare and delete this when we are done. Let me know once you see it. Or, if I can keep it to have the example for the developers that would be nice but certainly not required.

Thanks for reporting the problem so clearly! Helps to get a fast solution :scientist:

1 Like
4

Hey Jennaj,

Thanks for the help. I feel so silly for having a little optional name box to end up being my issue. I suppose it is not entirely optional then. Feel free to keep the copy for reporting to the devs. Cheers!

1 Like
5

Thanks! SO many tools, so many little options… We appreciate finding these things we can squash them :beetle: