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. 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