On Jun 7, 2013, at 9:44 AM, Daofeng Li <lid...@gmail.com> wrote:
> Dear R Community,
>
> I have encountered a problem while using the R function glm.nb.
> The code that produce the error was following two lines:
>
> group=c(1,1,1,1,0,0,0,0)
> fit=glm.nb(y~group)
>
> While the y contains 8 sets of number like:
> gene275 0 1 0 0 1 5 1 0
>
> Error message:
>
> Error in while ((it <- it + 1) < limit && abs(del) > eps) { :
> missing value where TRUE/FALSE needed
> Calls: glm.nb -> as.vector -> theta.ml
> In addition: There were 50 or more warnings (use warnings() to see the
> first 50)
> Execution halted
>
>
> Information of my system:
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> Does anyone happen to have some hit on how to solve this?
> Appreciate for any response.
>
> Thanks in advance,
>
> Daofeng
There is something wrong with your actual 'y' or 'group' that is not evident
from the above info:
group <- c(1, 1, 1, 1, 0, 0, 0, 0)
y <- c(0, 1, 0, 0, 1, 5, 1, 0)
> require(MASS)
Loading required package: MASS
> glm.nb(y ~ group)
Call: glm.nb(formula = y ~ group, init.theta = 1.711564307, link = log)
Coefficients:
(Intercept) group
0.5596 -1.9459
Degrees of Freedom: 7 Total (i.e. Null); 6 Residual
Null Deviance: 10.23
Residual Deviance: 6.848 AIC: 25.25
Check str(y) and str(group)
You should also be sure to note in your posts when you are using a function
from a non-base package, in this case MASS, which is not indicated in your
sessionInfo() above, so something is amiss there as well.
Regards,
Marc Schwartz
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