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liaoherui / GDmicro

GDmicro - Use GCN and Deep adaptation network to classify host disease status based on human gut microbiome data.
https://academic.oup.com/bioinformatics/article/39/12/btad747/7470738
MIT License
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run error #3

Closed gwcde closed 5 months ago

gwcde commented 5 months ago

676b7bc1eb23aa52d51bb07a9cdcaa4

python GDmicro.py -i Input_files/CRC_10fold.csv -t 1 -d CRC -o GDmicro_new_pipe/CRC_10fold There was an error running CRC dataset directly, and no modifications were made before execution.

liaoherui commented 5 months ago

Hi, thanks for using GDmicro!

The log shows that "Rscript" is not found. Have you installed all required packages with the conda command? (please see "Install" section of the README page)

gwcde commented 5 months ago

Thank you, now it runs successfully. In running 10-fold cross-validation, I found that the Area Under the Curve (AUC) result of each fold is determined by selecting the best AUC result from 150 epochs. d6e270099398bedbaefeef74db6c6fc

liaoherui commented 5 months ago

In practical applications, GDmicro strives to identify robust and accurate microbial markers that can effectively distinguish between case and control samples. Consequently, the program has been updated to implement the model with the highest performance, ensuring satisfactory results for this task.