Dear All, Firstly, I am new to both R and bioconductor, but I have tried to solve my problem with google, R FAQ and bioconductor help pages and not got anywhere. I have only installed R today, using this download http://cran.ma.imperial.ac.uk/bin/macosx/ I'm trying to run the affy package to analyse some HG-U133A2 data.... and have come across an error: "Error in R > eset <- mas5(Data) : object 'R' not found" Whilst trying to work out why I get the above message, and what might be missing I realise the following (from the sample workflow page): "Affymetrix 3'-biased Arrays affy, gcrma, affyPLM Require cdf package, probe package and annotation package All these packages are available from Bioconductor via biocLite()" However when trying to install all three of these packages I get the warning message "package is not available (for R version 2.13.2)" In the package list http://bioconductor.org/packages/release/bioc/ None of these three packages are listed for me to see if they run on OSX. Therefore I think I might be confused about these three packages and the earlier error I received running affy. Any clarification gratefully received. Thanks in advance for your help. Kind regards, -Sarah -- output of sessionInfo(): > library(affy) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation("pkgname")'. > Data <- ReadAffy() > eset <- rma(Data) Warning: unable to access index for repository http://brainarray.mbni. med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13 Warning: unable to access index for repository http://brainarray.mbni. med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13 trying URL 'http://bioconductor.org/packages/2.8/data/annotation/bin/m acosx/leopard/contrib/2.13/hgu133a2cdf_2.8.0.tgz' Content type 'application/x-gzip' length 1744432 bytes (1.7 Mb) opened URL ================================================== downloaded 1.7 Mb The downloaded packages are in /var/folders/uF/uFWwo07rEmKgKopLFvaXGk+++TI/-Tmp-//RtmpgL0vGe/ downloaded_packages Background correcting Normalizing Calculating Expression > eset <- expresso(Dilution, normalize.method="qspline", bgcorrect.method="rma",pmcorrect.method="pmonly", + summary.method="liwong") Error in expresso(Dilution, normalize.method = "qspline", bgcorrect.method = "rma", : object 'Dilution' not found > R> eset <- mas5(Data) background correction: mas PM/MM correction : mas expression values: mas background correcting...done. 22277 ids to be processed | | |####################| Error in R > eset <- mas5(Data) : object 'R' not found > biocLite("cdf") Error: could not find function "biocLite" > source("http://www.bioconductor.org/biocLite.R") BioC_mirror = http://bioconductor.org Change using chooseBioCmirror(). > biocLite("cdf") Using R version 2.13.2, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages: [1] "cdf" Please wait... Warning: unable to access index for repository http://brainarray.mbni. med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13 Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ???cdf??? is not available (for R version 2.13.2) > biocLIte("probe") Error: could not find function "biocLIte" > source("http://www.bioconductor.org/biocLite.R") BioC_mirror = http://bioconductor.org Change using chooseBioCmirror(). Warning messages: 1: In safeSource() : Redefining ???biocinstall??? 2: In safeSource() : Redefining ???biocinstallPkgGroups??? 3: In safeSource() : Redefining ???biocinstallRepos??? > biocLite("probe") Using R version 2.13.2, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages: [1] "probe" Please wait... Warning: unable to access index for repository http://brainarray.mbni. med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13 Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ???probe??? is not available (for R version 2.13.2) > biocLite("annotation") Using R version 2.13.2, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages: [1] "annotation" Please wait... Warning: unable to access index for repository http://brainarray.mbni. med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13 Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ???annotation??? is not available (for R version 2.13.2) > -- Sent via the guest posting facility at bioconductor.org.

You should not copy the "R>" part of whatever document you are using. The beginning "R>" just refers to the R prompt. Sometimes the R is left out, like ">" and in that case you should also not copy the ">". Kasper On Wed, Oct 12, 2011 at 11:24 AM, Sarah Little [guest] <guest at="" bioconductor.org=""> wrote: > > Dear All, > > Firstly, I am new to both R and bioconductor, but I have tried to solve my problem with google, R FAQ and bioconductor help pages and not got anywhere. > > I have only installed R today, using this download > http://cran.ma.imperial.ac.uk/bin/macosx/ > > I'm trying to run the affy package to analyse some HG-U133A2 data.... > > and have come across an error: > "Error in R > eset <- mas5(Data) : object 'R' not found" > > Whilst trying to work out why I get the above message, and what might be missing I realise the following (from the sample workflow page): > "Affymetrix 3'-biased Arrays > > affy, gcrma, affyPLM > Require cdf package, probe package and annotation package > All these packages are available from Bioconductor via biocLite()" > > However when trying to install all three of these packages I get the warning message > "package is not available (for R version 2.13.2)" > > In the package list http://bioconductor.org/packages/release/bioc/ > None of these three packages are listed for me to see if they run on OSX. > > Therefore I think I might be confused about these three packages and the earlier error I received running affy. > > > Any clarification gratefully received. > Thanks in advance for your help. > Kind regards, > > -Sarah > > ?-- output of sessionInfo(): > >> library(affy) > Loading required package: Biobase > > Welcome to Bioconductor > > ?Vignettes contain introductory material. To view, type > ?'browseVignettes()'. To cite Bioconductor, see > ?'citation("Biobase")' and for packages 'citation("pkgname")'. > >> Data <- ReadAffy() >> eset <- rma(Data) > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13 > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13 > trying URL 'http://bioconductor.org/packages/2.8/data/annotation/bin /macosx/leopard/contrib/2.13/hgu133a2cdf_2.8.0.tgz' > Content type 'application/x-gzip' length 1744432 bytes (1.7 Mb) > opened URL > ================================================== > downloaded 1.7 Mb > > > The downloaded packages are in > ? ? ? ?/var/folders/uF/uFWwo07rEmKgKopLFvaXGk+++TI/-Tmp-//RtmpgL0vGe /downloaded_packages > Background correcting > Normalizing > Calculating Expression >> eset <- expresso(Dilution, normalize.method="qspline", bgcorrect.method="rma",pmcorrect.method="pmonly", > + summary.method="liwong") > Error in expresso(Dilution, normalize.method = "qspline", bgcorrect.method = "rma", ?: > ?object 'Dilution' not found >> R> eset <- mas5(Data) > background correction: mas > PM/MM correction : mas > expression values: mas > background correcting...done. > 22277 ids to be processed > | ? ? ? ? ? ? ? ? ? ?| > |####################| > Error in R > eset <- mas5(Data) : object 'R' not found >> biocLite("cdf") > Error: could not find function "biocLite" >> source("http://www.bioconductor.org/biocLite.R") > BioC_mirror = http://bioconductor.org > Change using chooseBioCmirror(). >> biocLite("cdf") > Using R version 2.13.2, biocinstall version 2.8.4. > Installing Bioconductor version 2.8 packages: > [1] "cdf" > Please wait... > > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13 > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > ?package ???cdf??? is not available (for R version 2.13.2) >> biocLIte("probe") > Error: could not find function "biocLIte" >> source("http://www.bioconductor.org/biocLite.R") > BioC_mirror = http://bioconductor.org > Change using chooseBioCmirror(). > Warning messages: > 1: In safeSource() : Redefining ???biocinstall??? > 2: In safeSource() : Redefining ???biocinstallPkgGroups??? > 3: In safeSource() : Redefining ???biocinstallRepos??? >> biocLite("probe") > Using R version 2.13.2, biocinstall version 2.8.4. > Installing Bioconductor version 2.8 packages: > [1] "probe" > Please wait... > > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13 > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > ?package ???probe??? is not available (for R version 2.13.2) >> biocLite("annotation") > Using R version 2.13.2, biocinstall version 2.8.4. > Installing Bioconductor version 2.8 packages: > [1] "annotation" > Please wait... > > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13 > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > ?package ???annotation??? is not available (for R version 2.13.2) >> > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

Hi Sarah, Comments inline. On 10/12/2011 11:24 AM, Sarah Little [guest] wrote: > Dear All, > > Firstly, I am new to both R and bioconductor, but I have tried to solve my problem with google, R FAQ and bioconductor help pages and not got anywhere. > > I have only installed R today, using this download > http://cran.ma.imperial.ac.uk/bin/macosx/ > > I'm trying to run the affy package to analyse some HG-U133A2 data.... > > and have come across an error: > "Error in R> eset<- mas5(Data) : object 'R' not found" > > Whilst trying to work out why I get the above message, and what might be missing I realise the following (from the sample workflow page): > "Affymetrix 3'-biased Arrays > > affy, gcrma, affyPLM > Require cdf package, probe package and annotation package > All these packages are available from Bioconductor via biocLite()" In this workflow, the terms 'cdf', 'probe' and 'annotation' are used as general descriptive terms, not as actual package names. The correct cdf package will be installed automagically by the affy package, so you don't have to worry about that. If you want to install the annotation package, note that the name of the package will be hgu133a2.db, so something like library(BiocInstaller) biocLite("hgu133a2.db") will install it for you. The probe package will be called hgu133a2probe, and can be installed in a similar fashion. > > However when trying to install all three of these packages I get the warning message > "package is not available (for R version 2.13.2)" > > In the package list http://bioconductor.org/packages/release/bioc/ > None of these three packages are listed for me to see if they run on OSX. > > Therefore I think I might be confused about these three packages and the earlier error I received running affy. > > > Any clarification gratefully received. > Thanks in advance for your help. > Kind regards, > > -Sarah > > -- output of sessionInfo(): > >> library(affy) > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation("pkgname")'. > >> Data<- ReadAffy() >> eset<- rma(Data) > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13 > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13 > trying URL 'http://bioconductor.org/packages/2.8/data/annotation/bin /macosx/leopard/contrib/2.13/hgu133a2cdf_2.8.0.tgz' > Content type 'application/x-gzip' length 1744432 bytes (1.7 Mb) > opened URL > ================================================== > downloaded 1.7 Mb This part ^^^^^^^ is where the correct cdf package is installed. > > > The downloaded packages are in > /var/folders/uF/uFWwo07rEmKgKopLFvaXGk+++TI/-Tmp-//RtmpgL0vGe/ downloaded_packages > Background correcting > Normalizing > Calculating Expression >> eset<- expresso(Dilution, normalize.method="qspline", bgcorrect.method="rma",pmcorrect.method="pmonly", > + summary.method="liwong") > Error in expresso(Dilution, normalize.method = "qspline", bgcorrect.method = "rma", : > object 'Dilution' not found >> R> eset<- mas5(Data) > background correction: mas > PM/MM correction : mas > expression values: mas > background correcting...done. > 22277 ids to be processed > | | > |####################| > Error in R> eset<- mas5(Data) : object 'R' not found This looks like you copied the whole line, including the 'R >' prompt and then pasted into your R session. You don't want to include that first bit, as what this line translates to in 'R speak' is: Is some object 'R' greater than an object 'eset', which is created by running mas5() on an object called 'Data'. Since R couldn't find this 'R' object, it spit out the error saying it couldn't find it. Best, Jim >> biocLite("cdf") > Error: could not find function "biocLite" >> source("http://www.bioconductor.org/biocLite.R") > BioC_mirror = http://bioconductor.org > Change using chooseBioCmirror(). >> biocLite("cdf") > Using R version 2.13.2, biocinstall version 2.8.4. > Installing Bioconductor version 2.8 packages: > [1] "cdf" > Please wait... > > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13 > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ??~cdf??T is not available (for R version 2.13.2) >> biocLIte("probe") > Error: could not find function "biocLIte" >> source("http://www.bioconductor.org/biocLite.R") > BioC_mirror = http://bioconductor.org > Change using chooseBioCmirror(). > Warning messages: > 1: In safeSource() : Redefining ??~biocinstall??T > 2: In safeSource() : Redefining ??~biocinstallPkgGroups??T > 3: In safeSource() : Redefining ??~biocinstallRepos??T >> biocLite("probe") > Using R version 2.13.2, biocinstall version 2.8.4. > Installing Bioconductor version 2.8 packages: > [1] "probe" > Please wait... > > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13 > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ??~probe??T is not available (for R version 2.13.2) >> biocLite("annotation") > Using R version 2.13.2, biocinstall version 2.8.4. > Installing Bioconductor version 2.8 packages: > [1] "annotation" > Please wait... > > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13 > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ??~annotation??T is not available (for R version 2.13.2) > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. 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