[BioC] Error: could not find function "plotPCA"
Surles, Monique
msurles at msm.edu
Thu May 22 23:20:17 CEST 2014
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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