Hello, I upgraded R from 2.5.1 to 2.6 on Ubuntu this morning. However, when I ran normalization using printtiploess, it showed the following error. > MA2 <- normalizeWithinArrays(RG, method="printtiploess") Error in .C("lowess", x = as.double(xobs[o]), as.double(yobs[o]), nobs, : C symbol name "lowess" not in DLL for package "base" However, no error for the next one. > MA3 <- normalizeWithinArrays(RG, method="printtiploess", weights=weight) Any suggests are welcome! Tiandao

Hi Tiandao -- I'm guess that you updated R but not your Bioconductor packages -- please provide sessionInfo() in all posts! There are instructions for updating packages on the Bioconductor web site http://www.bioconductor.org/docs/install-howto.html at the bottom of the page: source("http://bioconductor.org/biocLite.R") biocLite("Biobase") library(Biobase) repos <- biocReposList() update.packages(repos=repos, ask=FALSE) You should be careful to do this in an R session that does not hae any packages attached, because attached packages cannot be updated. The bioconductor release is being finalized, so you might find it helpful to run update.packages again after the release. Please let the list know if this solves your problem. Martin Tiandao Li <tiandao.li at="" usm.edu=""> writes: > Hello, > > I upgraded R from 2.5.1 to 2.6 on Ubuntu this morning. However, when I ran > normalization using printtiploess, it showed the following error. > >> MA2 <- normalizeWithinArrays(RG, method="printtiploess") > Error in .C("lowess", x = as.double(xobs[o]), as.double(yobs[o]), nobs, : > C symbol name "lowess" not in DLL for package "base" > > However, no error for the next one. > >> MA3 <- normalizeWithinArrays(RG, method="printtiploess", weights=weight) > > Any suggests are welcome! > > Tiandao > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org

Yes, your limma (2.10.5) is suitable for R 2.5 or 2.5.1 but you are using R 2.6. You will need to update your packages, as outlined in the original response. Here's what my R 2.6 looks like after following those directions and then, in a new session, library(limma). Note the limma version number. > sessionInfo() R version 2.6.0 Patched (2007-10-04 r43081) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY =en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELE PHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_2.12.0 loaded via a namespace (and not attached): [1] rcompgen_0.1-15 Maritn Tiandao Li <tiandao.li at="" usm.edu=""> writes: > Hi Martin, > >> sessionInfo() > R version 2.6.0 (2007-10-03) > i486-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] MASS_7.2-36 statmod_1.3.1 limma_2.10.5 > > loaded via a namespace (and not attached): > [1] rcompgen_0.1-15 > > > > On Thu, 4 Oct 2007, Martin Morgan wrote: > > Hi Tiandao -- > > I'm guess that you updated R but not your Bioconductor packages -- > please provide sessionInfo() in all posts! There are instructions for > updating packages on the Bioconductor web site > > http://www.bioconductor.org/docs/install-howto.html > > at the bottom of the page: > > source("http://bioconductor.org/biocLite.R") > biocLite("Biobase") > library(Biobase) > repos <- biocReposList() > update.packages(repos=repos, ask=FALSE) > > You should be careful to do this in an R session that does not hae any > packages attached, because attached packages cannot be updated. > > The bioconductor release is being finalized, so you might find it > helpful to run update.packages again after the release. > > Please let the list know if this solves your problem. > > Martin > > Tiandao Li <tiandao.li at="" usm.edu=""> writes: > >> Hello, >> >> I upgraded R from 2.5.1 to 2.6 on Ubuntu this morning. However, when I ran >> normalization using printtiploess, it showed the following error. >> >>> MA2 <- normalizeWithinArrays(RG, method="printtiploess") >> Error in .C("lowess", x = as.double(xobs[o]), as.double(yobs[o]), nobs, : >> C symbol name "lowess" not in DLL for package "base" >> >> However, no error for the next one. >> >>> MA3 <- normalizeWithinArrays(RG, method="printtiploess", weights=weight) >> >> Any suggests are welcome! >> >> Tiandao >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > Martin Morgan > Bioconductor / Computational Biology > http://bioconductor.org > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org

Hi Tiandao There are likely to be minor changes prior to the release, so I would recommend updating packages (using the same procedure) shortly after when the release is announced. Martin Tiandao Li <tiandao.li at="" usm.edu=""> writes: > Hi Martin, > > I update BioC as you suggested, the problem is solved. One more question, > should I update BioC again after this Friday? > > Thanks, > > Tiandao > >> sessionInfo() > R version 2.6.0 (2007-10-03) > i486-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] limma_2.12.0 > > loaded via a namespace (and not attached): > [1] rcompgen_0.1-15 > > > > > On Thu, 4 Oct 2007, Martin Morgan wrote: > > Yes, your limma (2.10.5) is suitable for R 2.5 or 2.5.1 but you are > using R 2.6. > > You will need to update your packages, as outlined in the original > response. Here's what my R 2.6 looks like after following those > directions and then, in a new session, library(limma). Note the > limma version number. > >> sessionInfo() > R version 2.6.0 Patched (2007-10-04 r43081) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETA RY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TE LEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] limma_2.12.0 > > loaded via a namespace (and not attached): > [1] rcompgen_0.1-15 > > Maritn > > Tiandao Li <tiandao.li at="" usm.edu=""> writes: > >> Hi Martin, >> >>> sessionInfo() >> R version 2.6.0 (2007-10-03) >> i486-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_ US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT F-8;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] MASS_7.2-36 statmod_1.3.1 limma_2.10.5 >> >> loaded via a namespace (and not attached): >> [1] rcompgen_0.1-15 >> >> >> >> On Thu, 4 Oct 2007, Martin Morgan wrote: >> >> Hi Tiandao -- >> >> I'm guess that you updated R but not your Bioconductor packages -- >> please provide sessionInfo() in all posts! There are instructions for >> updating packages on the Bioconductor web site >> >> http://www.bioconductor.org/docs/install-howto.html >> >> at the bottom of the page: >> >> source("http://bioconductor.org/biocLite.R") >> biocLite("Biobase") >> library(Biobase) >> repos <- biocReposList() >> update.packages(repos=repos, ask=FALSE) >> >> You should be careful to do this in an R session that does not hae any >> packages attached, because attached packages cannot be updated. >> >> The bioconductor release is being finalized, so you might find it >> helpful to run update.packages again after the release. >> >> Please let the list know if this solves your problem. >> >> Martin >> >> Tiandao Li <tiandao.li at="" usm.edu=""> writes: >> >>> Hello, >>> >>> I upgraded R from 2.5.1 to 2.6 on Ubuntu this morning. However, when I ran >>> normalization using printtiploess, it showed the following error. >>> >>>> MA2 <- normalizeWithinArrays(RG, method="printtiploess") >>> Error in .C("lowess", x = as.double(xobs[o]), as.double(yobs[o]), nobs, : >>> C symbol name "lowess" not in DLL for package "base" >>> >>> However, no error for the next one. >>> >>>> MA3 <- normalizeWithinArrays(RG, method="printtiploess", weights=weight) >>> >>> Any suggests are welcome! >>> >>> Tiandao >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> -- >> Martin Morgan >> Bioconductor / Computational Biology >> http://bioconductor.org >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > Martin Morgan > Bioconductor / Computational Biology > http://bioconductor.org -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org