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)$coef[2,]) >> > } >> > } >> > qval = qvalue(result[,4]) >> > fdr=0.1 >> > index=(qval$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 ______________________________________________ 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.