Error using run_DE_analysis.pl

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Tikshana Yadav

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Sep 27, 2024, 5:49:41 AM9/27/24

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I tried following command:

/run_DE_analysis.pl --matrix BAG_Abiotic.matrix --method edgeR --dispersion 0.1 --output BAG_DE --contrasts contrasts.txt

had following error

CMD: R --vanilla -q < BAG_Abiotic.matrix.Control:0hr_vs_Control:1hr.Control:0hr.vs.Control:1hr.EdgeR.Rscript
sh: 1: R: not found
Error, cmd: R --vanilla -q < BAG_Abiotic.matrix.Control:0hr_vs_Control:1hr.Control:0hr.vs.Control:1hr.EdgeR.Rscript died with ret (32512) at /mnt/d/anaconda3/opt/trinity-2.1.1/Analysis/DifferentialExpression/run_DE_analysis.pl line 712.