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



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