I used to be able to call update() for lme objects. Now I get this error:> ge.lme <- update(ge.lme, data=dat)Error in update(ge.lme, data = dat) : No direct or inherited method for function "update" for this call Here is the relevant portion of my code: ge <- eset[1,] dat <- data.frame(age, gen, fdr, ge) ge.lme <- lme(fixed=ge~age+gen+age*gen, data=dat, random=~ 1| fdr) for (i in 1:nrow(eset)) { dat$ge <- c(eset[i,]) ge.lme <- update(ge.lme, data=dat) . . . } I am using: base 1.9.0 utils 1.9.0 graphics 1.9.0 stats 1.9.0 methods 1.9.0 Biobase 1.4.14 affy 1.4.30 gcrma 1.1.0 annaffy 1.0.7 KEGG 1.4.0 GO 1.5.1 mgu74av2 1.4.0 nlme 3.1-48 xtable 1.2-1 Any help or suggestions would be most appreciated. Thanks much, Dick ******************************************************************************* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
Prof Brian Ripley
2004-May-26 05:18 UTC
[R] No direct or inherited method for function "update"
Try doing this without all those Bioconductor packages loaded. It does work in base R, and I suspect that one of your packages has redefined update (by adding S4 methods?). If you track down exactly which package causes the problem, you can report it to the appropriate person. On Tue, 25 May 2004, Dick Beyer wrote:> I used to be able to call update() for lme objects. Now I get this error: > > > ge.lme <- update(ge.lme, data=dat) > Error in update(ge.lme, data = dat) : No direct or inherited method for function "update" for this call > > > Here is the relevant portion of my code: > > ge <- eset[1,] > dat <- data.frame(age, gen, fdr, ge) > ge.lme <- lme(fixed=ge~age+gen+age*gen, data=dat, random=~ 1| fdr) > for (i in 1:nrow(eset)) { > dat$ge <- c(eset[i,]) > ge.lme <- update(ge.lme, data=dat) > . > . > . > } > > I am using: > base 1.9.0 > utils 1.9.0 > graphics 1.9.0 > stats 1.9.0 > methods 1.9.0 > Biobase 1.4.14 > affy 1.4.30 > gcrma 1.1.0 > annaffy 1.0.7 > KEGG 1.4.0 > GO 1.5.1 > mgu74av2 1.4.0 > nlme 3.1-48 > xtable 1.2-1 > > Any help or suggestions would be most appreciated. > > Thanks much, > Dick > ******************************************************************************* > Richard P. Beyer, Ph.D. University of Washington > Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
Thanks very much for your help. Following your suggestion, I found that the offending bioconductor package is affy. I will report that to the bioconductor folks. ******************************************************************************* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html ******************************************************************************* On Wed, 26 May 2004, Prof Brian Ripley wrote:> Try doing this without all those Bioconductor packages loaded. It does > work in base R, and I suspect that one of your packages has redefined > update (by adding S4 methods?). If you track down exactly which package > causes the problem, you can report it to the appropriate person. > > On Tue, 25 May 2004, Dick Beyer wrote: > > > I used to be able to call update() for lme objects. Now I get this error: > > > > > ge.lme <- update(ge.lme, data=dat) > > Error in update(ge.lme, data = dat) : No direct or inherited method for function "update" for this call > > > > > > Here is the relevant portion of my code: > > > > ge <- eset[1,] > > dat <- data.frame(age, gen, fdr, ge) > > ge.lme <- lme(fixed=ge~age+gen+age*gen, data=dat, random=~ 1| fdr) > > for (i in 1:nrow(eset)) { > > dat$ge <- c(eset[i,]) > > ge.lme <- update(ge.lme, data=dat) > > . > > . > > . > > } > > > > I am using: > > base 1.9.0 > > utils 1.9.0 > > graphics 1.9.0 > > stats 1.9.0 > > methods 1.9.0 > > Biobase 1.4.14 > > affy 1.4.30 > > gcrma 1.1.0 > > annaffy 1.0.7 > > KEGG 1.4.0 > > GO 1.5.1 > > mgu74av2 1.4.0 > > nlme 3.1-48 > > xtable 1.2-1 > > > > Any help or suggestions would be most appreciated. > > > > Thanks much, > > Dick > > ******************************************************************************* > > Richard P. Beyer, Ph.D. University of Washington > > Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 > > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > > Seattle, WA 98105-6099 > > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > > > > ______________________________________________ > > R-help at stat.math.ethz.ch mailing list > > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > > > > > > -- > Brian D. Ripley, ripley at stats.ox.ac.uk > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UK Fax: +44 1865 272595 > >