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vahuynh / dynGENIE3

Semi-parametric approach for the inference of gene regulatory networks from time series of expression data
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Error using alpha = "from.data" #6

Closed M-Marku closed 10 months ago

M-Marku commented 1 year ago

Hi,

I am using dynGENIE3 on a 6-sample dataset, with 5 time points each. While setting alpha = fixed_value works perfectly, using alpha = "from.data" gives 

Error in { :
task 2 failed - "NA/NaN/Inf in foreign function call (arg 4)"

Any idea where this error comes from, and how to solve it? Thanks

vahuynh commented 1 year ago

Hi,

I would need a bit more info.

Could you run the following: alphas <- estimate.decay.rates(TS.data, time.points), where TS.data and time.points are the same input arguments as when calling dynGENIE3(TS.data, time.points), and check if alphashas some nan or inf values?

M-Marku commented 1 year ago

Indeed, there were a few NaN values of alphas for some genes. Thank you for your fast reply and your help.