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fogellab / multiWGCNA

an R package for deep mining gene co-expression networks in multi-trait expression data
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Preservation Error #16

Closed GettyScience closed 3 days ago

GettyScience commented 4 months ago

Hello, I have begun running into this error "Error in eval(expr, p) : object 'name2' not found while running the preservationComparisons function. It happened after I reopened R and uploaded a data save file.

Thank you,

dariotommasini commented 4 months ago

Hi @GettyScience

Not much I can do based on this info. Can you make a reproducible example using the data provided in the package?

GettyScience commented 4 months ago

When I run the below function, with my own data, I get the above error message. It runs for a while and then stops. I was successfully able to run this function before and have not changed any part of my dataset. The only change that occurred was that R died when my laptop died and when I reloaded the session, it was unable to run this function. All other functions appear to be working. I could try to run from a previous version of multiWGCNA and see if the problem is still there?

results$preservation=iterate(autism_networks[conditions1], # this does autism vs control; change to "conditions2" to perform comparison between FC and TC preservationComparisons, write=TRUE, plot=TRUE, nPermutations=10)

GettyScience commented 3 months ago

Hello,

I just wanted to let you know that the problem appears to me to be that the function getPreservation() is missing a formula for how to name "name2" and so when the file it produces calls for this "name2" it doesn't exist.

Thank you,

dariotommasini commented 3 months ago

Okay I'll look into this. Does this occur when using the example data as well? I'm pretty sure this function was working for others recently. Maybe update to the development version?

dariotommasini commented 3 weeks ago

Hi @GettyScience, I just wanted to check if you're still having this issue or if you've resolved it. I have not been able to reproduce it.