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
[[alternative HTML version deleted]]
Hi, On Fri, Jun 7, 2013 at 10:44 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 haltedI'd assume there is a missing value somewhere. But we really need a reproducible example to be certain. You could use dput(head(yourdata, 20)) to give us something to work with (as long as that much of your data throws the error). At the very least, we probably also need str(y) str(group) Are you certain there are no missing values in your data? The problem may not be that obvious, but that's an easy place to start. Sarah> > 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 >-- Sarah Goslee http://www.functionaldiversity.org
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, > > DaofengThere 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