Aldex2 plugin_error

Community Plugin Support
1

Dear @dgiguer,
Sorry for posting the same error that has been discussed already within the forum. However, I have read carefully and tired already the solution posted already in the forum.
I got the following error when I tried to run the aldex2.

"Plugin error from aldex2:
An error was encountered while running ALDEx2 in R (return code 1), please inspect stdout and stderr to learn more."

I have tried already solutions posted.

Usage: qiime aldex2 [OPTIONS] COMMAND [ARGS]...

Description: Analysis Of Differential Abundance Taking Sample Variation
Into Account

Plugin website: GitHub - ggloor/q2-aldex2: qiime2 plugin for aldex2 for differential abundance analysis

Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org

Options:
--version Show the version and exit.
--citations Show citations and exit.
--help Show this message and exit.

Commands:
aldex2 Analysis Of Differential Abundance
effect-plot Effect plots
extract-differences Extract differentially expressed features

Any help is would be perfect.

Selin

2

Hi @sln,

Somebody else might have some more helpful guidance here, but you will need to understand the error that is arising in R:

Error in apply(data[, grp1], 1, sd) : dim(X) must have a positive length

Researching this error will at least get you heading in the right direction.

3

Hi @andrewsanchez,
Thanks a lot for your suggestion.
All I can think is the Error is arising since I decreased the number of samples to test the workflow before the actual analysis. Of course, I will dig into more details.