Search
Question: Error: could not find function "plotPCA"
0
gravatar for Surles, Monique
4.4 years ago by
United States
Surles, Monique50 wrote:
Dear List, While affycoretools were loaded, I am unable to get plotPCA to work,. I am using Windows 7 Professional(32 bit). Error: could not find function "plotPCA" Please assist…Is there something I am missing? Thank you Some relevant excerpts from my session: version 3.0.3 (2014-03-06) -- "Warm Puppy" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > source("http://www.bioconductor.org/biocLite.R") Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help A newer version of Bioconductor is available after installing a new version of R, ?BiocUpgrade for help > biocLite("affy") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. Installing package(s) 'affy' trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/con trib/3.0/affy_1.40.0.zip' Content type 'application/zip' length 1462050 bytes (1.4 Mb) opened URL downloaded 1.4 Mb package ‘affy’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\msurles\AppData\Local\Temp\Rtmpq2i9qB\downloaded_packages > biocLite("affycoretools") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. Installing package(s) 'affycoretools' trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/con trib/3.0/affycoretools_1.34.0.zip' Content type 'application/zip' length 7060308 bytes (6.7 Mb) opened URL downloaded 6.7 Mb package ‘affycoretools’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\msurles\AppData\Local\Temp\Rtmpq2i9qB\downloaded_packages > biocLite("limma") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. Installing package(s) 'limma' trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/con trib/3.0/limma_3.18.13.zip' Content type 'application/zip' length 3190124 bytes (3.0 Mb) opened URL downloaded 3.0 Mb package ‘limma’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\msurles\AppData\Local\Temp\Rtmpq2i9qB\downloaded_packages > library(affy) Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > library(limma) Attaching package: ‘limma’ The following object is masked from ‘package:BiocGenerics’: plotMA > library(affycoretools) Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: DBI Loading required package: KEGG.db KEGG.db contains mappings based on older data because the original resource was removed from the the public domain before the most recent update was produced. This package should now be considered deprecated and future versions of Bioconductor may not have it available. Users who want more current data are encouraged to look at the KEGGREST or reactome.db packages KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘ff’ Error: package or namespace load failed for ‘affycoretools’ > > biocLite("affycoretools") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. Installing package(s) 'affycoretools' trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/con trib/3.0/affycoretools_1.34.0.zip' Content type 'application/zip' length 7060308 bytes (6.7 Mb) opened URL downloaded 6.7 Mb Calculating Expression > eset1 <- mas5(mydata) background correction: mas PM/MM correction : mas expression values: mas background correcting...done. 54675 ids to be processed | | |####################| > plotPCA(eset, groups = as.numeric(pData(mydata)[,1]), groupnames = levels(pData(mydata)[,1])) Error: could not find function "plotPCA" Thank you Monique PhD student [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.4 years ago by Michael Love19k • written 4.4 years ago by Surles, Monique50
0
gravatar for Michael Love
4.4 years ago by
Michael Love19k
United States
Michael Love19k wrote:
hi Monique, Were you able to load affycoretools without error? After library(affycoretools) You have Error: package or namespace load failed for ?affycoretools? Mike On Thu, May 22, 2014 at 5:04 PM, Surles, Monique <msurles at="" msm.edu=""> wrote: > Dear List, > > While affycoretools were loaded, I am unable to get plotPCA to work,. I am using Windows 7 Professional(32 bit). > > Error: could not find function "plotPCA" > Please assist?Is there something I am missing? Thank you > > > > Some relevant excerpts from > my session: > version 3.0.3 (2014-03-06) -- "Warm Puppy" > Copyright (C) 2014 The R Foundation for Statistical Computing > Platform: x86_64-w64-mingw32/x64 (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> source("http://www.bioconductor.org/biocLite.R") > Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help > A newer version of Bioconductor is available after installing a new version > of R, ?BiocUpgrade for help >> biocLite("affy") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. > Installing package(s) 'affy' > trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/c ontrib/3.0/affy_1.40.0.zip' > Content type 'application/zip' length 1462050 bytes (1.4 Mb) > opened URL > downloaded 1.4 Mb > > package ?affy? successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > C:\Users\msurles\AppData\Local\Temp\Rtmpq2i9qB\downloaded_packages >> biocLite("affycoretools") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. > Installing package(s) 'affycoretools' > trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/c ontrib/3.0/affycoretools_1.34.0.zip' > Content type 'application/zip' length 7060308 bytes (6.7 Mb) > opened URL > downloaded 6.7 Mb > > package ?affycoretools? successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > C:\Users\msurles\AppData\Local\Temp\Rtmpq2i9qB\downloaded_packages >> biocLite("limma") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. > Installing package(s) 'limma' > trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/c ontrib/3.0/limma_3.18.13.zip' > Content type 'application/zip' length 3190124 bytes (3.0 Mb) > opened URL > downloaded 3.0 Mb > > package ?limma? successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > C:\Users\msurles\AppData\Local\Temp\Rtmpq2i9qB\downloaded_packages >> library(affy) > Loading required package: BiocGenerics > Loading required package: parallel > > Attaching package: ?BiocGenerics? > > The following objects are masked from ?package:parallel?: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, clusterMap, parApply, parCapply, parLapply, > parLapplyLB, parRapply, parSapply, parSapplyLB > > The following object is masked from ?package:stats?: > > xtabs > > The following objects are masked from ?package:base?: > > anyDuplicated, append, as.data.frame, as.vector, cbind, > colnames, duplicated, eval, evalq, Filter, Find, get, > intersect, is.unsorted, lapply, Map, mapply, match, mget, > order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, > rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, > tapply, union, unique, unlist > > Loading required package: Biobase > Welcome to Bioconductor > > Vignettes contain introductory material; view with > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")', and for packages 'citation("pkgname")'. > >> library(limma) > > Attaching package: ?limma? > > The following object is masked from ?package:BiocGenerics?: > > plotMA > >> library(affycoretools) > Loading required package: GO.db > Loading required package: AnnotationDbi > Loading required package: DBI > > Loading required package: KEGG.db > > KEGG.db contains mappings based on older data because the original > resource was removed from the the public domain before the most > recent update was produced. This package should now be considered > deprecated and future versions of Bioconductor may not have it > available. Users who want more current data are encouraged to > look at the KEGGREST or reactome.db packages > > KernSmooth 2.23 loaded > Copyright M. P. Wand 1997-2009 > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : > there is no package called ?ff? > Error: package or namespace load failed for ?affycoretools? >> >> biocLite("affycoretools") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. > Installing package(s) 'affycoretools' > trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/c ontrib/3.0/affycoretools_1.34.0.zip' > Content type 'application/zip' length 7060308 bytes (6.7 Mb) > opened URL > downloaded 6.7 Mb > > > > Calculating Expression > >> eset1 <- mas5(mydata) > > background correction: mas > > PM/MM correction : mas > > expression values: mas > > background correcting...done. > > 54675 ids to be processed > > | | > > |####################| > >> plotPCA(eset, groups = as.numeric(pData(mydata)[,1]), groupnames = levels(pData(mydata)[,1])) > > Error: could not find function "plotPCA" > > > Thank you > > Monique > PhD student > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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
ADD COMMENTlink written 4.4 years ago by Michael Love19k
Hi Micheal, No, there is still an after library(affycoretools) Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ?ff? Error: package or namespace load failed for ?affycoretools? Monique -----Original Message----- From: Michael Love [mailto:michaelisaiahlove@gmail.com] Sent: Thursday, May 22, 2014 5:14 PM To: Surles, Monique Cc: bioconductor at r-project.org Subject: Re: [BioC] Error: could not find function "plotPCA" hi Monique, Were you able to load affycoretools without error? After library(affycoretools) You have Error: package or namespace load failed for ?affycoretools? Mike On Thu, May 22, 2014 at 5:04 PM, Surles, Monique <msurles at="" msm.edu=""> wrote: > Dear List, > > While affycoretools were loaded, I am unable to get plotPCA to work,. I am using Windows 7 Professional(32 bit). > > Error: could not find function "plotPCA" > Please assist?Is there something I am missing? Thank you > > > > Some relevant excerpts from > my session: > version 3.0.3 (2014-03-06) -- "Warm Puppy" > Copyright (C) 2014 The R Foundation for Statistical Computing > Platform: x86_64-w64-mingw32/x64 (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and 'citation()' on how to > cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> source("http://www.bioconductor.org/biocLite.R") > Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help A > newer version of Bioconductor is available after installing a new version > of R, ?BiocUpgrade for help >> biocLite("affy") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. > Installing package(s) 'affy' > trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/c ontrib/3.0/affy_1.40.0.zip' > Content type 'application/zip' length 1462050 bytes (1.4 Mb) opened > URL downloaded 1.4 Mb > > package ?affy? successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > > C:\Users\msurles\AppData\Local\Temp\Rtmpq2i9qB\downloaded_packages >> biocLite("affycoretools") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. > Installing package(s) 'affycoretools' > trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/c ontrib/3.0/affycoretools_1.34.0.zip' > Content type 'application/zip' length 7060308 bytes (6.7 Mb) opened > URL downloaded 6.7 Mb > > package ?affycoretools? successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > > C:\Users\msurles\AppData\Local\Temp\Rtmpq2i9qB\downloaded_packages >> biocLite("limma") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. > Installing package(s) 'limma' > trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/c ontrib/3.0/limma_3.18.13.zip' > Content type 'application/zip' length 3190124 bytes (3.0 Mb) opened > URL downloaded 3.0 Mb > > package ?limma? successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > > C:\Users\msurles\AppData\Local\Temp\Rtmpq2i9qB\downloaded_packages >> library(affy) > Loading required package: BiocGenerics Loading required package: > parallel > > Attaching package: ?BiocGenerics? > > The following objects are masked from ?package:parallel?: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, clusterMap, parApply, parCapply, parLapply, > parLapplyLB, parRapply, parSapply, parSapplyLB > > The following object is masked from ?package:stats?: > > xtabs > > The following objects are masked from ?package:base?: > > anyDuplicated, append, as.data.frame, as.vector, cbind, > colnames, duplicated, eval, evalq, Filter, Find, get, > intersect, is.unsorted, lapply, Map, mapply, match, mget, > order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, > rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, > tapply, union, unique, unlist > > Loading required package: Biobase > Welcome to Bioconductor > > Vignettes contain introductory material; view with > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")', and for packages 'citation("pkgname")'. > >> library(limma) > > Attaching package: ?limma? > > The following object is masked from ?package:BiocGenerics?: > > plotMA > >> library(affycoretools) > Loading required package: GO.db > Loading required package: AnnotationDbi Loading required package: DBI > > Loading required package: KEGG.db > > KEGG.db contains mappings based on older data because the original > resource was removed from the the public domain before the most > recent update was produced. This package should now be considered > deprecated and future versions of Bioconductor may not have it > available. Users who want more current data are encouraged to > look at the KEGGREST or reactome.db packages > > KernSmooth 2.23 loaded > Copyright M. P. Wand 1997-2009 > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : > there is no package called ?ff? > Error: package or namespace load failed for ?affycoretools? >> >> biocLite("affycoretools") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. > Installing package(s) 'affycoretools' > trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/c ontrib/3.0/affycoretools_1.34.0.zip' > Content type 'application/zip' length 7060308 bytes (6.7 Mb) opened > URL downloaded 6.7 Mb > > > > Calculating Expression > >> eset1 <- mas5(mydata) > > background correction: mas > > PM/MM correction : mas > > expression values: mas > > background correcting...done. > > 54675 ids to be processed > > | | > > |####################| > >> plotPCA(eset, groups = as.numeric(pData(mydata)[,1]), groupnames = >> levels(pData(mydata)[,1])) > > Error: could not find function "plotPCA" > > > Thank you > > Monique > PhD student > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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
ADD REPLYlink written 4.4 years ago by Surles, Monique50
Hi Monique, Try biocLite(c("oligo","affycoretools")) and let us know if that helps. Best, Jim On Thursday, May 22, 2014 5:20:17 PM, Surles, Monique wrote: > Hi Micheal, > No, there is still an after library(affycoretools) > > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : > there is no package called ?ff? > Error: package or namespace load failed for ?affycoretools? > > Monique > > -----Original Message----- > From: Michael Love [mailto:michaelisaiahlove at gmail.com] > Sent: Thursday, May 22, 2014 5:14 PM > To: Surles, Monique > Cc: bioconductor at r-project.org > Subject: Re: [BioC] Error: could not find function "plotPCA" > > hi Monique, > > Were you able to load affycoretools without error? > > After > > library(affycoretools) > > You have > > Error: package or namespace load failed for ?affycoretools? > > Mike > > On Thu, May 22, 2014 at 5:04 PM, Surles, Monique <msurles at="" msm.edu=""> wrote: >> Dear List, >> >> While affycoretools were loaded, I am unable to get plotPCA to work,. I am using Windows 7 Professional(32 bit). >> >> Error: could not find function "plotPCA" >> Please assist?Is there something I am missing? Thank you >> >> >> >> Some relevant excerpts from >> my session: >> version 3.0.3 (2014-03-06) -- "Warm Puppy" >> Copyright (C) 2014 The R Foundation for Statistical Computing >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> >> R is free software and comes with ABSOLUTELY NO WARRANTY. >> You are welcome to redistribute it under certain conditions. >> Type 'license()' or 'licence()' for distribution details. >> >> R is a collaborative project with many contributors. >> Type 'contributors()' for more information and 'citation()' on how to >> cite R or R packages in publications. >> >> Type 'demo()' for some demos, 'help()' for on-line help, or >> 'help.start()' for an HTML browser interface to help. >> Type 'q()' to quit R. >> >>> source("http://www.bioconductor.org/biocLite.R") >> Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help A >> newer version of Bioconductor is available after installing a new version >> of R, ?BiocUpgrade for help >>> biocLite("affy") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. >> Installing package(s) 'affy' >> trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/ contrib/3.0/affy_1.40.0.zip' >> Content type 'application/zip' length 1462050 bytes (1.4 Mb) opened >> URL downloaded 1.4 Mb >> >> package ?affy? successfully unpacked and MD5 sums checked >> >> The downloaded binary packages are in >> >> C:\Users\msurles\AppData\Local\Temp\Rtmpq2i9qB\downloaded_packages >>> biocLite("affycoretools") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. >> Installing package(s) 'affycoretools' >> trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/ contrib/3.0/affycoretools_1.34.0.zip' >> Content type 'application/zip' length 7060308 bytes (6.7 Mb) opened >> URL downloaded 6.7 Mb >> >> package ?affycoretools? successfully unpacked and MD5 sums checked >> >> The downloaded binary packages are in >> >> C:\Users\msurles\AppData\Local\Temp\Rtmpq2i9qB\downloaded_packages >>> biocLite("limma") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. >> Installing package(s) 'limma' >> trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/ contrib/3.0/limma_3.18.13.zip' >> Content type 'application/zip' length 3190124 bytes (3.0 Mb) opened >> URL downloaded 3.0 Mb >> >> package ?limma? successfully unpacked and MD5 sums checked >> >> The downloaded binary packages are in >> >> C:\Users\msurles\AppData\Local\Temp\Rtmpq2i9qB\downloaded_packages >>> library(affy) >> Loading required package: BiocGenerics Loading required package: >> parallel >> >> Attaching package: ?BiocGenerics? >> >> The following objects are masked from ?package:parallel?: >> >> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >> clusterExport, clusterMap, parApply, parCapply, parLapply, >> parLapplyLB, parRapply, parSapply, parSapplyLB >> >> The following object is masked from ?package:stats?: >> >> xtabs >> >> The following objects are masked from ?package:base?: >> >> anyDuplicated, append, as.data.frame, as.vector, cbind, >> colnames, duplicated, eval, evalq, Filter, Find, get, >> intersect, is.unsorted, lapply, Map, mapply, match, mget, >> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, >> rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, >> tapply, union, unique, unlist >> >> Loading required package: Biobase >> Welcome to Bioconductor >> >> Vignettes contain introductory material; view with >> 'browseVignettes()'. To cite Bioconductor, see >> 'citation("Biobase")', and for packages 'citation("pkgname")'. >> >>> library(limma) >> >> Attaching package: ?limma? >> >> The following object is masked from ?package:BiocGenerics?: >> >> plotMA >> >>> library(affycoretools) >> Loading required package: GO.db >> Loading required package: AnnotationDbi Loading required package: DBI >> >> Loading required package: KEGG.db >> >> KEGG.db contains mappings based on older data because the original >> resource was removed from the the public domain before the most >> recent update was produced. This package should now be considered >> deprecated and future versions of Bioconductor may not have it >> available. Users who want more current data are encouraged to >> look at the KEGGREST or reactome.db packages >> >> KernSmooth 2.23 loaded >> Copyright M. P. Wand 1997-2009 >> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : >> there is no package called ?ff? >> Error: package or namespace load failed for ?affycoretools? >>> >>> biocLite("affycoretools") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. >> Installing package(s) 'affycoretools' >> trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/ contrib/3.0/affycoretools_1.34.0.zip' >> Content type 'application/zip' length 7060308 bytes (6.7 Mb) opened >> URL downloaded 6.7 Mb >> >> >> >> Calculating Expression >> >>> eset1 <- mas5(mydata) >> >> background correction: mas >> >> PM/MM correction : mas >> >> expression values: mas >> >> background correcting...done. >> >> 54675 ids to be processed >> >> | | >> >> |####################| >> >>> plotPCA(eset, groups = as.numeric(pData(mydata)[,1]), groupnames = >>> levels(pData(mydata)[,1])) >> >> Error: could not find function "plotPCA" >> >> >> Thank you >> >> Monique >> PhD student >> >> >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> 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 > _______________________________________________ > 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. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD REPLYlink written 4.4 years ago by James W. MacDonald48k
Hi Jim, Thank you so much.....it worked. Monique -----Original Message----- From: James W. MacDonald [mailto:jmacdon@uw.edu] Sent: Thursday, May 22, 2014 5:31 PM To: Surles, Monique Cc: bioconductor at r-project.org; Michael Love Subject: Re: [BioC] Error: could not find function "plotPCA" Hi Monique, Try biocLite(c("oligo","affycoretools")) and let us know if that helps. Best, Jim On Thursday, May 22, 2014 5:20:17 PM, Surles, Monique wrote: > Hi Micheal, > No, there is still an after library(affycoretools) > > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : > there is no package called ?ff? > Error: package or namespace load failed for ?affycoretools? > > Monique > > -----Original Message----- > From: Michael Love [mailto:michaelisaiahlove at gmail.com] > Sent: Thursday, May 22, 2014 5:14 PM > To: Surles, Monique > Cc: bioconductor at r-project.org > Subject: Re: [BioC] Error: could not find function "plotPCA" > > hi Monique, > > Were you able to load affycoretools without error? > > After > > library(affycoretools) > > You have > > Error: package or namespace load failed for ?affycoretools? > > Mike > > On Thu, May 22, 2014 at 5:04 PM, Surles, Monique <msurles at="" msm.edu=""> wrote: >> Dear List, >> >> While affycoretools were loaded, I am unable to get plotPCA to work,. I am using Windows 7 Professional(32 bit). >> >> Error: could not find function "plotPCA" >> Please assist?Is there something I am missing? Thank you >> >> >> >> Some relevant excerpts from >> my session: >> version 3.0.3 (2014-03-06) -- "Warm Puppy" >> Copyright (C) 2014 The R Foundation for Statistical Computing >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> >> R is free software and comes with ABSOLUTELY NO WARRANTY. >> You are welcome to redistribute it under certain conditions. >> Type 'license()' or 'licence()' for distribution details. >> >> R is a collaborative project with many contributors. >> Type 'contributors()' for more information and 'citation()' on how to >> cite R or R packages in publications. >> >> Type 'demo()' for some demos, 'help()' for on-line help, or >> 'help.start()' for an HTML browser interface to help. >> Type 'q()' to quit R. >> >>> source("http://www.bioconductor.org/biocLite.R") >> Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help >> A newer version of Bioconductor is available after installing a new version >> of R, ?BiocUpgrade for help >>> biocLite("affy") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. >> Installing package(s) 'affy' >> trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/ contrib/3.0/affy_1.40.0.zip' >> Content type 'application/zip' length 1462050 bytes (1.4 Mb) opened >> URL downloaded 1.4 Mb >> >> package ?affy? successfully unpacked and MD5 sums checked >> >> The downloaded binary packages are in >> >> C:\Users\msurles\AppData\Local\Temp\Rtmpq2i9qB\downloaded_packages >>> biocLite("affycoretools") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. >> Installing package(s) 'affycoretools' >> trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/ contrib/3.0/affycoretools_1.34.0.zip' >> Content type 'application/zip' length 7060308 bytes (6.7 Mb) opened >> URL downloaded 6.7 Mb >> >> package ?affycoretools? successfully unpacked and MD5 sums checked >> >> The downloaded binary packages are in >> >> C:\Users\msurles\AppData\Local\Temp\Rtmpq2i9qB\downloaded_packages >>> biocLite("limma") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. >> Installing package(s) 'limma' >> trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/ contrib/3.0/limma_3.18.13.zip' >> Content type 'application/zip' length 3190124 bytes (3.0 Mb) opened >> URL downloaded 3.0 Mb >> >> package ?limma? successfully unpacked and MD5 sums checked >> >> The downloaded binary packages are in >> >> C:\Users\msurles\AppData\Local\Temp\Rtmpq2i9qB\downloaded_packages >>> library(affy) >> Loading required package: BiocGenerics Loading required package: >> parallel >> >> Attaching package: ?BiocGenerics? >> >> The following objects are masked from ?package:parallel?: >> >> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >> clusterExport, clusterMap, parApply, parCapply, parLapply, >> parLapplyLB, parRapply, parSapply, parSapplyLB >> >> The following object is masked from ?package:stats?: >> >> xtabs >> >> The following objects are masked from ?package:base?: >> >> anyDuplicated, append, as.data.frame, as.vector, cbind, >> colnames, duplicated, eval, evalq, Filter, Find, get, >> intersect, is.unsorted, lapply, Map, mapply, match, mget, >> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, >> rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, >> tapply, union, unique, unlist >> >> Loading required package: Biobase >> Welcome to Bioconductor >> >> Vignettes contain introductory material; view with >> 'browseVignettes()'. To cite Bioconductor, see >> 'citation("Biobase")', and for packages 'citation("pkgname")'. >> >>> library(limma) >> >> Attaching package: ?limma? >> >> The following object is masked from ?package:BiocGenerics?: >> >> plotMA >> >>> library(affycoretools) >> Loading required package: GO.db >> Loading required package: AnnotationDbi Loading required package: DBI >> >> Loading required package: KEGG.db >> >> KEGG.db contains mappings based on older data because the original >> resource was removed from the the public domain before the most >> recent update was produced. This package should now be considered >> deprecated and future versions of Bioconductor may not have it >> available. Users who want more current data are encouraged to >> look at the KEGGREST or reactome.db packages >> >> KernSmooth 2.23 loaded >> Copyright M. P. Wand 1997-2009 >> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : >> there is no package called ?ff? >> Error: package or namespace load failed for ?affycoretools? >>> >>> biocLite("affycoretools") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.3. >> Installing package(s) 'affycoretools' >> trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/ contrib/3.0/affycoretools_1.34.0.zip' >> Content type 'application/zip' length 7060308 bytes (6.7 Mb) opened >> URL downloaded 6.7 Mb >> >> >> >> Calculating Expression >> >>> eset1 <- mas5(mydata) >> >> background correction: mas >> >> PM/MM correction : mas >> >> expression values: mas >> >> background correcting...done. >> >> 54675 ids to be processed >> >> | | >> >> |####################| >> >>> plotPCA(eset, groups = as.numeric(pData(mydata)[,1]), groupnames = >>> levels(pData(mydata)[,1])) >> >> Error: could not find function "plotPCA" >> >> >> Thank you >> >> Monique >> PhD student >> >> >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> 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 > _______________________________________________ > 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. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD REPLYlink written 4.4 years ago by Surles, Monique50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 391 users visited in the last hour