[BioC] Error: could not find function "plotPCA"
James W. MacDonald
jmacdon at uw.edu
Thu May 22 23:31:09 CEST 2014
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]]
>>
>>
>> _______________________________________________
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> _______________________________________________
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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