glm.nb error
On Jun 7, 2013, at 9:44 AM, Daofeng Li <lidaof at 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