Hi Ioannis

Perhaps there is a 0 value, which is passed inside the function, needed to
compute some internal functions. It may explains lack of convergence in
glm.fit function.
I hope that this helps,

Alok

On Tue, Jun 28, 2011 at 12:18 AM, Filippis, Ioannis <
i.filippis@imperial.ac.uk> wrote:

> Hi,
>
> I am trying to run fitNbinomGLMs but depending on the factor selected, it
> gives error "Error: NA/NaN/Inf in foreign function call (arg 1)".
> The counts matrix doesn't have any Na/NaN values, I cannot really
> understand what the problem is. I guess it shouldn't work for any factor if
> there was any problem with gene counts.
>
> > pData(cdsFull)
>     sizeFactor condition type
> wtH1 2.17904027   treated    a
> wtP1 0.24260614   treated    b
> prH1 1.42343596 untreated    a
> prP1 0.14120460 untreated    b
> wtH4 3.45554434   treated    a
> wtP4 2.38048956   treated    b
> prH4 4.13642641 untreated    a
> prP4 0.40209227 untreated    b
> wtH7 3.76575182   treated    a
> wtP7 0.88389937   treated    b
> prH7 2.98917685 untreated    a
> prP7 0.08601356 untreated    b
> > head(counts(cdsFull))
>  wtH1 wtP1 prH1 prP1 wtH4 wtP4 prH4 prP4 wtH7 wtP7 prH7 prP7
> 1   12    3    5    0   12   30   10    0    8   11   11    0
> 2  195   14   99    0   14   31   38    2   36   12   39    1
> 3  135   25  112   15  482  252  321   34  233   73  175    4
> 4  149   11  119   22  525  181  828   92  998  181 1086   19
> 5    6    0    8    0    5    3    3    0    2    0   12    0
> 6   39    2    4   21   77  120   26  192   35   15    6   11
>
> > fit0<-fitNbinomGLMs(cdsFull, count ~ type)
> .............
> There were 26 warnings (use warnings() to see them)
> > fit1<-fitNbinomGLMs(cdsFull, count ~ condition)
> ..........Error: NA/NaN/Inf in foreign function call (arg 1)
> In addition: There were 21 warnings (use warnings() to see them)
> > fit1<-fitNbinomGLMs(cdsFull, count ~ condition + type)
> Error: NA/NaN/Inf in foreign function call (arg 1)
> In addition: Warning message:
> glm.fit: algorithm did not converge
>
> Many thanks for your help.
>
> Best,
> Ioannis
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-- 
************************************************************
Alok Kumar Srivastava
Ph.D scholar
Centre of Computational Biology and Bioinformatics
School of Computational and Integrative Sciences
JNU, New Delhi
************************************************************

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