[BioC] DESeq - fitNbinomGLMs - Error: NA/NaN/Inf in foreign function call

[Filippis, Ioannis]

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