De novo differential expression error: print(resultsfiles) : object 'resultsfiles' not found

[Guillermo Marco Puche]

Hello Edu,

I'm getting the following error on the final step of the miRNA de-novo pipeline. I can't identify the cause of this error. I'm following the miRNA de-novo example posted here:

http://miarmaseq.idoproteins.com/examples

I'm using latest version from repo. I've tried to see what happens in R without luck. All libraries seem to be installed correctly. I attach also a log from R session, I've got stuck on this error on three different machines with R 3.4.1, 3.4.3 and 3.4.4 all resulting in the same error.

[Eduardo Andres Leon]

Hi, which miARma version are you using ? I see this in your R log: 2016 IBIS when you should see miARma version 1.7.3 2018 IBIS & IPBLN.

Besides, what happened if you include rpkm="yes" in the DEAnalysis section

[Guillermo Marco Puche]

Hi, I'm using latest repo version:

curl -L -O https://bitbucket.org/cbbio/miarma/get/master.tar.bz2
tar -xjf master.tar.bz2
cd cbbio-miarma-54d2dc0fdd81/
nohup ./miARma Examples/basic_examples/miRNAs/DeNovo_miRNAs/miARma_miRNAs_DeNovo.ini &

Already tried adding rpkm="yes" to the config file and I get the exact same error.

I attach the log I get from console when executing basic miRNA de_novo example

[Eduardo Andres Leon]

ummm curious because according with your log file, rpkm=no

resultsfiles<-DE_EdgeR(projectdir="/media/Data/miarma_181126/cbbio-miarma-54d2dc0fdd81/Examples/basic_examples/miRNAs/DeNovo_miRNAs/results/EdgeR_results",dir="/media/Data/miarma_181126/cbbio-miarma-54d2dc0fdd81/Examples/basic_examples/miRNAs/DeNovo_miRNAs/results/DeNovo_ReadCount", file="/media/Data/miarma_181126/cbbio-miarma-54d2dc0fdd81/Examples/basic_examples/miRNAs/DeNovo_miRNAs/results/DeNovo_ReadCount/miRNAs.tab", targetfile="/media/Data/miarma_181126/cbbio-miarma-54d2dc0fdd81/Examples/basic_examples/miRNAs/data/targets.txt", label="Hypoxia_miRNAs.tab", contrastfile="/media/Data/miarma_181126/cbbio-miarma-54d2dc0fdd81/Examples/basic_examples/miRNAs/data/contrast.txt", filter="yes", replicates="yes", rpkm="no", file_size="/media/Data/miarma_181126/cbbio-miarma-54d2dc0fdd81/Examples/basic_examples/miRNAs/DeNovo_miRNAs/results/DeNovo_Size/miRNAs.tab", cpm="yes")

Let me execute the whole pipeline as you have done in order to test that everything is fine from my side

[Guillermo Marco Puche]

Yes this log execution is without rpkm set in config, but it should work aswell right? I'm using default config provided in examples. I can run with rpkm="yes" if you want and provide log, but I was getting the exact same error.

[Eduardo Andres Leon]

Hi again, I'm not 100% sure yet but I think you have found a bug related to the rpkm calculation

I'll let you now as soon as possible (and I'll fix the software)

Thanks a lot

[Guillermo Marco Puche]

Thank you very much. It's really weird because differential expression is working well with known miRNA pipeline.

[Guillermo Marco Puche]

In the meantime do you think I can use any old versión with de-novo differential expression working?

[Eduardo Andres Leon]

I think so: https://sourceforge.net/projects/miarma/files/miARmaSeq/miARma_v1.6.1/