vahuynh / dyngenie3 Goto Github PK

1. A warning signed that variable may be used uninitialized occur when i complie C code with 'R CMD SHLIB dynGENIE3.c'. It's a root that lead to the next error in the fig2.
   

2. LoadLibrary failure with the dynGENIE3.so
   

I'll appreciate your help, if you can reply me on your convenience.

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

Hi,

I was wondering if there was a way to visualize an AUROC plot (TPs vs. FPs) for a given gene regulatory network (GRN) constructed by the dynGENIE3 framework. If there isn't an easily available function, are there other ways to perform such a procedure? Any clarification would be greatly appreciated!

Best,
Rohak

Is there a minimum number of time points required to run this? I have 3 time points with 3, 3, and 2 replicates. I get this error
res <- dynGENIE3(TS.data, time.points)
Error in (num.samples.count + 1):(num.samples.count + num.samples.current) :
argument of length 0

Hello,

I was hoping that you would have time to give some advice on how to input different conditions and replicates to dynGENIE3. I'm successfully running the R implementation on my time series RNAseq data. However, I'm not quite sure the recommended way to input the different replicates and conditions.

My data is:
6 time points
8 conditions plus control
2-3 replicates per condition.

The way I am doing it now, I am inputting each condition and replicate as a separate time series and treating control as a separate condition and running them all at once. Do you recommend this, or to separate conditions into different runs and perhaps treat the control as steady state data?

Thank you for the helpful tool!
Best,
Rebecca