[R] glm.nb error
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:
gene2750 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-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_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]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] glm.nb error
Hi,
On Fri, Jun 7, 2013 at 10:44 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:
gene2750 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
I'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-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_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
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] glm.nb error
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:
gene2750 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-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_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: 6.848AIC: 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
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] glm.nb error
On Jun 7, 2013, at 10:36 AM, Daofeng Li lid...@gmail.com wrote:
Thank you Sarah and Marc for your fast and nice response.
Apology for didn't include all information.
I have a input file like following:
gene1 18 15 13 13 16 9 20 24
gene2 15 8 8 7 0 12 18 4
gene3 10 9 8 12 9 11 12 12
gene4 4 0 4 3 0 5 0 0
gene5 0 1 0 0 1 5 1 0
gene6 3 3 3 3 4 4 4 4
gene7 0 4 0 2 2 2 0 0
gene8 4 4 7 3 0 6 6 12
gene9 11 6 13 10 13 7 12 9
gene106 3 6 3 4 7 6 3
I am using following R code to compare the difference between the 1st 4
numbers against 2nd 4 numbers:
library(MASS)
library(coin)
suppressPackageStartupMessages(suppressWarnings(library(tcltk)))
library(qvalue)
library(plyr)
dat =
read.table(test,col.names=c(gene,b1,b2,b3,b4,c1,c2,c3,c4))
index=(apply(dat[,-1],1,sum)0)
data = dat[index,]
group=c(1,1,1,1,0,0,0,0)
n=nrow(data)
result=NULL
for (i in 1:n){
print(i)
y=as.numeric(data[i,-1])
if (all((y-mean(y))==0))
result=rbind(result,c(0,0,0,1))
else {
fit=glm.nb(y~group)
result=rbind(result,summary(fit)$coef[2,])
}
}
qval = qvalue(result[,4])
fdr=0.1
index=(qval$qvaluesfdr)
dat.result = data[index,]
write.table(dat.result,file=test_result,row.names=F,quote=F)
If you use this input file and code, would reproduce the same error:
Loading required package: methods
Loading required package: survival
Loading required package: splines
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Attaching package: ‘plyr’
The following object is masked from ‘package:modeltools’:
empty
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
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: Warning messages:
1: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace
:
iteration limit reached
2: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace
:
iteration limit reached
Execution halted
So might be the error was in 6th line, not the line I pasted before (5th
line)? Sorry about that.
Thanks.
Daofeng
Your 'y' at that point in the loop is:
y
[1] 3 3 3 3 4 4 4 4
and 'group' is:
group
[1] 1 1 1 1 0 0 0 0
glm.nb(y ~ group)
Error in while ((it - it + 1) limit abs(del) eps) { :
missing value where TRUE/FALSE needed
Think about it... :-)
Regards,
Marc Schwartz
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] glm.nb error
Hi,
On Fri, Jun 7, 2013 at 11:36 AM, Daofeng Li lid...@gmail.com wrote:
Thank you Sarah and Marc for your fast and nice response.
Apology for didn't include all information.
I have a input file like following:
gene1 18 15 13 13 16 9 20 24
gene2 15 8 8 7 0 12 18 4
gene3 10 9 8 12 9 11 12 12
gene4 4 0 4 3 0 5 0 0
gene5 0 1 0 0 1 5 1 0
gene6 3 3 3 3 4 4 4 4
gene7 0 4 0 2 2 2 0 0
gene8 4 4 7 3 0 6 6 12
gene9 11 6 13 10 13 7 12 9
gene10 6 3 6 3 4 7 6 3
dat =
read.table(test,col.names=c(gene,b1,b2,b3,b4,c1,c2,c3,c4))
Is this what's in the test file that your code reads in? We don't
have that file, so can't run your code.
If it is, then the output of
dput(dat)
would be enormously more useful than copy and pasting your data file
into your email.
And yes, the full code is very little like the pair of lines you
originally pasted in.
Sarah
I am using following R code to compare the difference between the 1st 4
numbers against 2nd 4 numbers:
library(MASS)
library(coin)
suppressPackageStartupMessages(suppressWarnings(library(tcltk)))
library(qvalue)
library(plyr)
dat =
read.table(test,col.names=c(gene,b1,b2,b3,b4,c1,c2,c3,c4))
index=(apply(dat[,-1],1,sum)0)
data = dat[index,]
group=c(1,1,1,1,0,0,0,0)
n=nrow(data)
result=NULL
for (i in 1:n){
print(i)
y=as.numeric(data[i,-1])
if (all((y-mean(y))==0))
result=rbind(result,c(0,0,0,1))
else {
fit=glm.nb(y~group)
result=rbind(result,summary(fit)$coef[2,])
}
}
qval = qvalue(result[,4])
fdr=0.1
index=(qval$qvaluesfdr)
dat.result = data[index,]
write.table(dat.result,file=test_result,row.names=F,quote=F)
If you use this input file and code, would reproduce the same error:
Loading required package: methods
Loading required package: survival
Loading required package: splines
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Attaching package: ‘plyr’
The following object is masked from ‘package:modeltools’:
empty
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
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: Warning messages:
1: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace =
control$trace :
iteration limit reached
2: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace =
control$trace :
iteration limit reached
Execution halted
So might be the error was in 6th line, not the line I pasted before (5th
line)? Sorry about that.
Thanks.
Daofeng
On Fri, Jun 7, 2013 at 10:15 AM, Marc Schwartz marc_schwa...@me.com wrote:
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:
gene2750 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-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_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: 6.848AIC: 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
--
Sarah Goslee
http://www.functionaldiversity.org
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
Re: [R] glm.nb error
As Marc already pointed out, take a close look at this part of your loop:
R i - 6
R
R y - as.numeric(data[i,-1])
R y
[1] 3 3 3 3 4 4 4 4
R group
[1] 1 1 1 1 0 0 0 0
R fit - glm.nb(y~group)
Error in while ((it - it + 1) limit abs(del) eps) { :
missing value where TRUE/FALSE needed
What do you expect to happen there?
In general, it's a better practice to pre-specify the size of result
(eg matrix(NA, nrow=n, ncol=4) ) and fill it as you go, rather than
using rbind() within a loop. Much more memory-efficient.
Sarah
On Fri, Jun 7, 2013 at 11:58 AM, Daofeng Li lid...@gmail.com wrote:
Sorry Sarah.
dput(dat)
structure(list(gene = structure(c(1L, 3L, 4L, 5L, 6L, 7L, 8L,
9L, 10L, 2L), .Label = c(gene1, gene10, gene2, gene3,
gene4, gene5, gene6, gene7, gene8, gene9), class = factor),
b1 = c(18L, 15L, 10L, 4L, 0L, 3L, 0L, 4L, 11L, 6L), b2 = c(15L,
8L, 9L, 0L, 1L, 3L, 4L, 4L, 6L, 3L), b3 = c(13L, 8L, 8L,
4L, 0L, 3L, 0L, 7L, 13L, 6L), b4 = c(13L, 7L, 12L, 3L, 0L,
3L, 2L, 3L, 10L, 3L), c1 = c(16L, 0L, 9L, 0L, 1L, 4L, 2L,
0L, 13L, 4L), c2 = c(9L, 12L, 11L, 5L, 5L, 4L, 2L, 6L, 7L,
7L), c3 = c(20L, 18L, 12L, 0L, 1L, 4L, 0L, 6L, 12L, 6L),
c4 = c(24L, 4L, 12L, 0L, 0L, 4L, 0L, 12L, 9L, 3L)), .Names = c(gene,
b1, b2, b3, b4, c1, c2, c3, c4), class = data.frame,
row.names = c(NA,
-10L))
above was the dput(dat). Thanks.
Daofeng
On Fri, Jun 7, 2013 at 10:47 AM, Sarah Goslee sarah.gos...@gmail.com
wrote:
Hi,
On Fri, Jun 7, 2013 at 11:36 AM, Daofeng Li lid...@gmail.com wrote:
Thank you Sarah and Marc for your fast and nice response.
Apology for didn't include all information.
I have a input file like following:
gene1 18 15 13 13 16 9 20 24
gene2 15 8 8 7 0 12 18 4
gene3 10 9 8 12 9 11 12 12
gene4 4 0 4 3 0 5 0 0
gene5 0 1 0 0 1 5 1 0
gene6 3 3 3 3 4 4 4 4
gene7 0 4 0 2 2 2 0 0
gene8 4 4 7 3 0 6 6 12
gene9 11 6 13 10 13 7 12 9
gene10 6 3 6 3 4 7 6 3
dat =
read.table(test,col.names=c(gene,b1,b2,b3,b4,c1,c2,c3,c4))
Is this what's in the test file that your code reads in? We don't
have that file, so can't run your code.
If it is, then the output of
dput(dat)
would be enormously more useful than copy and pasting your data file
into your email.
And yes, the full code is very little like the pair of lines you
originally pasted in.
Sarah
I am using following R code to compare the difference between the 1st 4
numbers against 2nd 4 numbers:
library(MASS)
library(coin)
suppressPackageStartupMessages(suppressWarnings(library(tcltk)))
library(qvalue)
library(plyr)
dat =
read.table(test,col.names=c(gene,b1,b2,b3,b4,c1,c2,c3,c4))
index=(apply(dat[,-1],1,sum)0)
data = dat[index,]
group=c(1,1,1,1,0,0,0,0)
n=nrow(data)
result=NULL
for (i in 1:n){
print(i)
y=as.numeric(data[i,-1])
if (all((y-mean(y))==0))
result=rbind(result,c(0,0,0,1))
else {
fit=glm.nb(y~group)
result=rbind(result,summary(fit)$coef[2,])
}
}
qval = qvalue(result[,4])
fdr=0.1
index=(qval$qvaluesfdr)
dat.result = data[index,]
write.table(dat.result,file=test_result,row.names=F,quote=F)
If you use this input file and code, would reproduce the same error:
Loading required package: methods
Loading required package: survival
Loading required package: splines
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Attaching package: ‘plyr’
The following object is masked from ‘package:modeltools’:
empty
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
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: Warning messages:
1: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace =
control$trace :
iteration limit reached
2: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace =
control$trace :
iteration limit reached
Execution halted
So might be the error was in 6th line, not the line I pasted before (5th
line)? Sorry about that.
Thanks.
Daofeng
On Fri, Jun 7, 2013 at 10:15 AM, Marc Schwartz marc_schwa...@me.com
wrote:
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:
gene2750 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
Re: [R] glm.nb error
Sorry Sarah.
dput(dat)
structure(list(gene = structure(c(1L, 3L, 4L, 5L, 6L, 7L, 8L,
9L, 10L, 2L), .Label = c(gene1, gene10, gene2, gene3,
gene4, gene5, gene6, gene7, gene8, gene9), class = factor),
b1 = c(18L, 15L, 10L, 4L, 0L, 3L, 0L, 4L, 11L, 6L), b2 = c(15L,
8L, 9L, 0L, 1L, 3L, 4L, 4L, 6L, 3L), b3 = c(13L, 8L, 8L,
4L, 0L, 3L, 0L, 7L, 13L, 6L), b4 = c(13L, 7L, 12L, 3L, 0L,
3L, 2L, 3L, 10L, 3L), c1 = c(16L, 0L, 9L, 0L, 1L, 4L, 2L,
0L, 13L, 4L), c2 = c(9L, 12L, 11L, 5L, 5L, 4L, 2L, 6L, 7L,
7L), c3 = c(20L, 18L, 12L, 0L, 1L, 4L, 0L, 6L, 12L, 6L),
c4 = c(24L, 4L, 12L, 0L, 0L, 4L, 0L, 12L, 9L, 3L)), .Names = c(gene,
b1, b2, b3, b4, c1, c2, c3, c4), class = data.frame,
row.names = c(NA,
-10L))
above was the dput(dat). Thanks.
Daofeng
On Fri, Jun 7, 2013 at 10:47 AM, Sarah Goslee sarah.gos...@gmail.comwrote:
Hi,
On Fri, Jun 7, 2013 at 11:36 AM, Daofeng Li lid...@gmail.com wrote:
Thank you Sarah and Marc for your fast and nice response.
Apology for didn't include all information.
I have a input file like following:
gene1 18 15 13 13 16 9 20 24
gene2 15 8 8 7 0 12 18 4
gene3 10 9 8 12 9 11 12 12
gene4 4 0 4 3 0 5 0 0
gene5 0 1 0 0 1 5 1 0
gene6 3 3 3 3 4 4 4 4
gene7 0 4 0 2 2 2 0 0
gene8 4 4 7 3 0 6 6 12
gene9 11 6 13 10 13 7 12 9
gene10 6 3 6 3 4 7 6 3
dat =
read.table(test,col.names=c(gene,b1,b2,b3,b4,c1,c2,c3,c4))
Is this what's in the test file that your code reads in? We don't
have that file, so can't run your code.
If it is, then the output of
dput(dat)
would be enormously more useful than copy and pasting your data file
into your email.
And yes, the full code is very little like the pair of lines you
originally pasted in.
Sarah
I am using following R code to compare the difference between the 1st 4
numbers against 2nd 4 numbers:
library(MASS)
library(coin)
suppressPackageStartupMessages(suppressWarnings(library(tcltk)))
library(qvalue)
library(plyr)
dat =
read.table(test,col.names=c(gene,b1,b2,b3,b4,c1,c2,c3,c4))
index=(apply(dat[,-1],1,sum)0)
data = dat[index,]
group=c(1,1,1,1,0,0,0,0)
n=nrow(data)
result=NULL
for (i in 1:n){
print(i)
y=as.numeric(data[i,-1])
if (all((y-mean(y))==0))
result=rbind(result,c(0,0,0,1))
else {
fit=glm.nb(y~group)
result=rbind(result,summary(fit)$coef[2,])
}
}
qval = qvalue(result[,4])
fdr=0.1
index=(qval$qvaluesfdr)
dat.result = data[index,]
write.table(dat.result,file=test_result,row.names=F,quote=F)
If you use this input file and code, would reproduce the same error:
Loading required package: methods
Loading required package: survival
Loading required package: splines
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Attaching package: plyr
The following object is masked from package:modeltools:
empty
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
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: Warning messages:
1: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace =
control$trace :
iteration limit reached
2: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace =
control$trace :
iteration limit reached
Execution halted
So might be the error was in 6th line, not the line I pasted before (5th
line)? Sorry about that.
Thanks.
Daofeng
On Fri, Jun 7, 2013 at 10:15 AM, Marc Schwartz marc_schwa...@me.com
wrote:
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:
gene2750 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-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_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
Re: [R] glm.nb error
Thank you Sarah and Marc for your fast and nice response.
Apology for didn't include all information.
I have a input file like following:
gene1 18 15 13 13 16 9 20 24
gene2 15 8 8 7 0 12 18 4
gene3 10 9 8 12 9 11 12 12
gene4 4 0 4 3 0 5 0 0
gene5 0 1 0 0 1 5 1 0
gene6 3 3 3 3 4 4 4 4
gene7 0 4 0 2 2 2 0 0
gene8 4 4 7 3 0 6 6 12
gene9 11 6 13 10 13 7 12 9
gene10 6 3 6 3 4 7 6 3
I am using following R code to compare the difference between the 1st 4
numbers against 2nd 4 numbers:
library(MASS)
library(coin)
suppressPackageStartupMessages(suppressWarnings(library(tcltk)))
library(qvalue)
library(plyr)
dat =
read.table(test,col.names=c(gene,b1,b2,b3,b4,c1,c2,c3,c4))
index=(apply(dat[,-1],1,sum)0)
data = dat[index,]
group=c(1,1,1,1,0,0,0,0)
n=nrow(data)
result=NULL
for (i in 1:n){
print(i)
y=as.numeric(data[i,-1])
if (all((y-mean(y))==0))
result=rbind(result,c(0,0,0,1))
else {
fit=glm.nb(y~group)
result=rbind(result,summary(fit)$coef[2,])
}
}
qval = qvalue(result[,4])
fdr=0.1
index=(qval$qvaluesfdr)
dat.result = data[index,]
write.table(dat.result,file=test_result,row.names=F,quote=F)
If you use this input file and code, would reproduce the same error:
Loading required package: methods
Loading required package: survival
Loading required package: splines
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Attaching package: plyr
The following object is masked from package:modeltools:
empty
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
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: Warning messages:
1: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace =
control$trace :
iteration limit reached
2: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace =
control$trace :
iteration limit reached
Execution halted
So might be the error was in 6th line, not the line I pasted before (5th
line)? Sorry about that.
Thanks.
Daofeng
On Fri, Jun 7, 2013 at 10:15 AM, Marc Schwartz marc_schwa...@me.com wrote:
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:
gene2750 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-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_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: 6.848AIC: 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
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] glm.nb error
Thanks Marc...still didn't get it...
Tried this...
str(group)
num [1:8] 1 1 1 1 0 0 0 0
fit=glm.nb(y~group)
Error in while ((it - it + 1) limit abs(del) eps) { :
missing value where TRUE/FALSE needed
group - c('1','1','1','1','0','0','0','0')
str(group)
chr [1:8] 1 1 1 1 0 0 0 0
fit=glm.nb(y~group)
Error in while ((it - it + 1) limit abs(del) eps) { :
missing value where TRUE/FALSE needed
Daofeng
On Fri, Jun 7, 2013 at 10:48 AM, Marc Schwartz marc_schwa...@me.com wrote:
On Jun 7, 2013, at 10:36 AM, Daofeng Li lid...@gmail.com wrote:
Thank you Sarah and Marc for your fast and nice response.
Apology for didn't include all information.
I have a input file like following:
gene1 18 15 13 13 16 9 20 24
gene2 15 8 8 7 0 12 18 4
gene3 10 9 8 12 9 11 12 12
gene4 4 0 4 3 0 5 0 0
gene5 0 1 0 0 1 5 1 0
gene6 3 3 3 3 4 4 4 4
gene7 0 4 0 2 2 2 0 0
gene8 4 4 7 3 0 6 6 12
gene9 11 6 13 10 13 7 12 9
gene106 3 6 3 4 7 6 3
I am using following R code to compare the difference between the 1st 4
numbers against 2nd 4 numbers:
library(MASS)
library(coin)
suppressPackageStartupMessages(suppressWarnings(library(tcltk)))
library(qvalue)
library(plyr)
dat =
read.table(test,col.names=c(gene,b1,b2,b3,b4,c1,c2,c3,c4))
index=(apply(dat[,-1],1,sum)0)
data = dat[index,]
group=c(1,1,1,1,0,0,0,0)
n=nrow(data)
result=NULL
for (i in 1:n){
print(i)
y=as.numeric(data[i,-1])
if (all((y-mean(y))==0))
result=rbind(result,c(0,0,0,1))
else {
fit=glm.nb(y~group)
result=rbind(result,summary(fit)$coef[2,])
}
}
qval = qvalue(result[,4])
fdr=0.1
index=(qval$qvaluesfdr)
dat.result = data[index,]
write.table(dat.result,file=test_result,row.names=F,quote=F)
If you use this input file and code, would reproduce the same error:
Loading required package: methods
Loading required package: survival
Loading required package: splines
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Attaching package: plyr
The following object is masked from package:modeltools:
empty
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
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: Warning messages:
1: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace =
control$trace :
iteration limit reached
2: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace =
control$trace :
iteration limit reached
Execution halted
So might be the error was in 6th line, not the line I pasted before (5th
line)? Sorry about that.
Thanks.
Daofeng
Your 'y' at that point in the loop is:
y
[1] 3 3 3 3 4 4 4 4
and 'group' is:
group
[1] 1 1 1 1 0 0 0 0
glm.nb(y ~ group)
Error in while ((it - it + 1) limit abs(del) eps) { :
missing value where TRUE/FALSE needed
Think about it... :-)
Regards,
Marc Schwartz
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] glm.nb error
Thanks for all your help. I will try to fix this.
Very helpful.
Best,
Daofeng
On Fri, Jun 7, 2013 at 11:25 AM, Sarah Goslee sarah.gos...@gmail.comwrote:
As Marc already pointed out, take a close look at this part of your loop:
R i - 6
R
R y - as.numeric(data[i,-1])
R y
[1] 3 3 3 3 4 4 4 4
R group
[1] 1 1 1 1 0 0 0 0
R fit - glm.nb(y~group)
Error in while ((it - it + 1) limit abs(del) eps) { :
missing value where TRUE/FALSE needed
What do you expect to happen there?
In general, it's a better practice to pre-specify the size of result
(eg matrix(NA, nrow=n, ncol=4) ) and fill it as you go, rather than
using rbind() within a loop. Much more memory-efficient.
Sarah
On Fri, Jun 7, 2013 at 11:58 AM, Daofeng Li lid...@gmail.com wrote:
Sorry Sarah.
dput(dat)
structure(list(gene = structure(c(1L, 3L, 4L, 5L, 6L, 7L, 8L,
9L, 10L, 2L), .Label = c(gene1, gene10, gene2, gene3,
gene4, gene5, gene6, gene7, gene8, gene9), class = factor),
b1 = c(18L, 15L, 10L, 4L, 0L, 3L, 0L, 4L, 11L, 6L), b2 = c(15L,
8L, 9L, 0L, 1L, 3L, 4L, 4L, 6L, 3L), b3 = c(13L, 8L, 8L,
4L, 0L, 3L, 0L, 7L, 13L, 6L), b4 = c(13L, 7L, 12L, 3L, 0L,
3L, 2L, 3L, 10L, 3L), c1 = c(16L, 0L, 9L, 0L, 1L, 4L, 2L,
0L, 13L, 4L), c2 = c(9L, 12L, 11L, 5L, 5L, 4L, 2L, 6L, 7L,
7L), c3 = c(20L, 18L, 12L, 0L, 1L, 4L, 0L, 6L, 12L, 6L),
c4 = c(24L, 4L, 12L, 0L, 0L, 4L, 0L, 12L, 9L, 3L)), .Names =
c(gene,
b1, b2, b3, b4, c1, c2, c3, c4), class = data.frame,
row.names = c(NA,
-10L))
above was the dput(dat). Thanks.
Daofeng
On Fri, Jun 7, 2013 at 10:47 AM, Sarah Goslee sarah.gos...@gmail.com
wrote:
Hi,
On Fri, Jun 7, 2013 at 11:36 AM, Daofeng Li lid...@gmail.com wrote:
Thank you Sarah and Marc for your fast and nice response.
Apology for didn't include all information.
I have a input file like following:
gene1 18 15 13 13 16 9 20 24
gene2 15 8 8 7 0 12 18 4
gene3 10 9 8 12 9 11 12 12
gene4 4 0 4 3 0 5 0 0
gene5 0 1 0 0 1 5 1 0
gene6 3 3 3 3 4 4 4 4
gene7 0 4 0 2 2 2 0 0
gene8 4 4 7 3 0 6 6 12
gene9 11 6 13 10 13 7 12 9
gene10 6 3 6 3 4 7 6 3
dat =
read.table(test,col.names=c(gene,b1,b2,b3,b4,c1,c2,c3,c4))
Is this what's in the test file that your code reads in? We don't
have that file, so can't run your code.
If it is, then the output of
dput(dat)
would be enormously more useful than copy and pasting your data file
into your email.
And yes, the full code is very little like the pair of lines you
originally pasted in.
Sarah
I am using following R code to compare the difference between the 1st
4
numbers against 2nd 4 numbers:
library(MASS)
library(coin)
suppressPackageStartupMessages(suppressWarnings(library(tcltk)))
library(qvalue)
library(plyr)
dat =
read.table(test,col.names=c(gene,b1,b2,b3,b4,c1,c2,c3,c4))
index=(apply(dat[,-1],1,sum)0)
data = dat[index,]
group=c(1,1,1,1,0,0,0,0)
n=nrow(data)
result=NULL
for (i in 1:n){
print(i)
y=as.numeric(data[i,-1])
if (all((y-mean(y))==0))
result=rbind(result,c(0,0,0,1))
else {
fit=glm.nb(y~group)
result=rbind(result,summary(fit)$coef[2,])
}
}
qval = qvalue(result[,4])
fdr=0.1
index=(qval$qvaluesfdr)
dat.result = data[index,]
write.table(dat.result,file=test_result,row.names=F,quote=F)
If you use this input file and code, would reproduce the same error:
Loading required package: methods
Loading required package: survival
Loading required package: splines
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Attaching package: plyr
The following object is masked from package:modeltools:
empty
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
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: Warning messages:
1: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace =
control$trace :
iteration limit reached
2: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace =
control$trace :
iteration limit reached
Execution halted
So might be the error was in 6th line, not the line I pasted before
(5th
line)? Sorry about that.
Thanks.
Daofeng
On Fri, Jun 7, 2013 at 10:15 AM, Marc Schwartz marc_schwa...@me.com
wrote:
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:
gene2750 1 0 0 1 5 1
0
Error message:
