Hello all. I am working on some code for my lab and I have run into an error message I can seem to get around. My goal is to test each variable in the model given all other variables are present. Here is the code and the error that are tripping me up.

DESrun=nbinomLRT(DESrun, useOptim=FALSE, maxit = 500 reduced=as.formula(paste("~",paste(Vars[-i],collapse="+"))))

Error in optim(betaRow, objectiveFn, method = "L-BFGS-B", lower = -large, :

L-BFGS-B needs finite values of 'fn'

Vars contain my variables of interest, for example Vars = c("Age","Gender","Disorder"). And DESrun has my full model, dispersion estimates, size factor estimates, and data. I am using DESeq2 version 1.0.18.

If I am still getting this error with the useOptim set to false and maxit set to 500 anyone have a suggestion?

Thanks,

Todd

DESrun=nbinomLRT(DESrun, useOptim=FALSE, maxit = 500 reduced=as.formula(paste("~",paste(Vars[-i],collapse="+"))))

Error in optim(betaRow, objectiveFn, method = "L-BFGS-B", lower = -large, :

L-BFGS-B needs finite values of 'fn'

Vars contain my variables of interest, for example Vars = c("Age","Gender","Disorder"). And DESrun has my full model, dispersion estimates, size factor estimates, and data. I am using DESeq2 version 1.0.18.

If I am still getting this error with the useOptim set to false and maxit set to 500 anyone have a suggestion?

Thanks,

Todd

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