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Issue in creating scLVM object (Python execution error) #31

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ChadMDC opened this issue Nov 16, 2020 · 0 comments
Open

Issue in creating scLVM object (Python execution error) #31

ChadMDC opened this issue Nov 16, 2020 · 0 comments

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@ChadMDC
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ChadMDC commented Nov 16, 2020

Error Message: python.exec(paste(objName, " = scLVM(Y,geneID=geneID,tech_noise=tech_noise)", : name 'scLVM' is not defined

I am currently trying to work through the tutorial on scLVM package for R and running into the above error message when I try to create an sclvm object (line# 137 of scLVM_vignette.Rmd). I have been able to create the fitTechnicalNoise object (needed for sclvm object). However, when I try to use it to initialise the sclvm object the above error was obtained.

Reading some of the previous issues they suggested that the version of rPython seems to be the issue. My current rPython version is 0.0-6. I have also set the code to check that the versions match. Included is the running suggestions that was posted previously. These I have executed as well.

Previous Running suggestions:
Suggested help: python --version
export RPYTHON_PYTHON_VERSION="2.7.16"
R CMD INSTALL /Users/chadwatson/Downloads/rPython_0.0-6.tar.gz

I have also tried using smaller matrices,changing fitType of fitTechnicalNoise object, all of which resulting in the same python.exec error from line#137 of the tutorial. Is there a way for me to fix this issue to proceed in the tutorial?

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