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califano-lab / ARACNe-AP

Network Reverse Engineering through AP inference of Mutual Information
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Empty output #3

Open reshu23 opened 5 years ago

reshu23 commented 5 years ago

Hi,

I am running aracne.jar on my data set. But It is not generating output. First step: I calculated MI threshold. That was fine. After that, I used: java -Xmx5G -jar aracne.jar -e test/matrix.txt -o outputFolder --tfs test/tfs.txt --pvalue 1E-8 --seed 1, for single bootstrap, but output file was empty. I have attached my data set testMatrix.txt testTFS.txt

with this issue.

jmj21-ic commented 2 years ago

Hi,

I am experiencing the same issue when trying to run ARACNe-AP, and my files are highly similar to reshu23 (although my 'gene' column is lower case and I am using ENSEMBL ids). I have tried removing the ENSG letters from the ID so the column data is numeric as in the example. Any help would be highly appreciated!

Many thanks,

Jess

adeslatt commented 6 months ago

I have a similar problem of an empty output. Is it because of a minimum set of samples required? A little confusing since the other published paper mentioned that even a single sample could be used. This repository has been untouched for 7 years so i do not feel its being actively maintained @califino-lab. I was hoping to use viper but it does not appear that that is possible not to have the adj file created.