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)$coef[2,])
> > }
> > }
> > qval = qvalue(result[,4])
> > fdr=0.1
> > index=(qval$qvalues<fdr)
> > 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:
> >> > 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
> >>
> >
>
>
>
> --
> Sarah Goslee
> http://www.functionaldiversity.org
>
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