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markowetzlab / CNsignatures

This is data and code from our first paper on copy number signatures (Macintyre et al., Nat Gen, 2018).
https://www.nature.com/articles/s41588-018-0179-8?proof=trueInJun
MIT License
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No convergence in mixture model #3

Open vymao opened 4 years ago

vymao commented 4 years ago

I am trying to follow the steps of the analysis to fit the mixture models on my own dataset. However, I cannot seem to get the mixture model fitting to converge, even with 20 samples: 

> all_components<-fitMixtureModels(CN_features)
2 : *
3 : *
4 : *
5 : *
6 : *
7 : *
8 : *
9 : *
10 : *
2 : *
3 : *
4 : *
5 : *
6 : *
7 : *
8 : *
9 : *
10 : *
2 : *
3 : *
4 : *
5 : *
6 : *
7 : *
8 : *
9 : *
10 : *
2 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
     1 Log-likelihood: NA

3 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
     1 Log-likelihood: NA

4 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
     1 Log-likelihood: NA

5 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
     1 Log-likelihood: NA

6 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
     1 Log-likelihood: NA

7 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
     1 Log-likelihood: NA

8 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
     1 Log-likelihood: NA

9 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
     1 Log-likelihood: NA

10 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
     1 Log-likelihood: NA

Error in flexmix::stepFlexmix(dat ~ 1, model = flexmix::FLXMCmvpois(),  : 
  no convergence to a suitable mixture

Am I doing something wrong, or should I be using more samples?

vymao commented 4 years ago

I tried using other copy number data and got another error message: 

3 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
    12 Log-likelihood: NaN

4 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
    11 Log-likelihood: NaN

5 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
    11 Log-likelihood: NaN

6 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
    11 Log-likelihood: NaN

7 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
    11 Log-likelihood: NaN

8 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
    11 Log-likelihood: NaN

9 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
    10 Log-likelihood: NaN

10 : *Error in FLXfit(model = model, concomitant = concomitant, control = control,  : 
    11 Log-likelihood: NaN

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'getModel' for signature '"flexmix"'