Entering edit mode
Dear List,
I am unable to use rma() to process my data. I am using Windows 7 Professional(32 bit).Please assist. Is it because of the pd.ragene.2.0st warning message? Did I miss something? Thank you for your help.
Warning message: package ‘pd.ragene.2.0.st’ was built under R version 3.2.0
Warning message:
'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
Some relevant excerpts from
my session:
R version 3.1.3 (2015-03-09) -- "Smooth Sidewalk"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
> source("http://www.bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.2), ?biocLite for help
> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] pd.ragene.2.0.st_3.10.0 RSQLite_1.0.0 DBI_0.3.1 limma_3.22.7
[5] oligo_1.30.0 Biostrings_2.34.1 XVector_0.6.0 IRanges_2.0.1
[9] S4Vectors_0.4.0 Biobase_2.26.0 oligoClasses_1.28.0 BiocGenerics_0.12.1
[13] BiocInstaller_1.16.2
loaded via a namespace (and not attached):
[1] affxparser_1.38.0 affyio_1.34.0 bit_1.1-12 codetools_0.2-11 ff_2.2-13
[6] foreach_1.4.2 GenomeInfoDb_1.2.4 GenomicRanges_1.18.4 iterators_1.0.7 preprocessCore_1.28.0
[11] splines_3.1.3 tools_3.1.3 zlibbioc_1.12.0
>package ‘oligo’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\msurles\AppData\Local\Temp\RtmpA7V3aP\downloaded_packages
Old packages: 'manipulate', 'lattice'
Update all/some/none? [a/s/n]:
a
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.1/manipulate_1.0.1.zip'
Content type 'application/zip' length 35784 bytes (34 KB)
opened URL
downloaded 34 KB
package ‘manipulate’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\msurles\AppData\Local\Temp\RtmpA7V3aP\downloaded_packages
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.1/lattice_0.20-31.zip'
Content type 'application/zip' length 729806 bytes (712 KB)
opened URL
downloaded 712 KB
package ‘lattice’ successfully unpacked and MD5 sums checked
> library("oligo")
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, do.call, 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, unsplit
Loading required package: oligoClasses
Welcome to oligoClasses version 1.28.0
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")'.
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: XVector
============================================================================================================================================
Welcome to oligo version 1.30.0
============================================================================================================================================
Attaching package: ‘oligo’
The following object is masked from ‘package:BiocGenerics’:
normalize
> biocLite("limma")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.2), R version 3.1.3.
Installing package(s) 'limma'
trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/limma_3.22.7.zip'
Content type 'application/zip' length 4628474 bytes (4.4 MB)
opened URL
downloaded 4.4 MB
package ‘limma’ successfully unpacked and MD5 sums checked
> library("limma")
Attaching package: ‘limma’
The following object is masked from ‘package:oligo’:
backgroundCorrect
The following object is masked from ‘package:BiocGenerics’:
plotMA
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.2), ?biocLite for help
> biocLite("pd.ragene.2.0.st")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.2), R version 3.1.3.
Installing package(s) 'pd.ragene.2.0.st'
trying URL 'http://bioconductor.org/packages/3.0/data/annotation/bin/windows/contrib/3.1/pd.ragene.2.0.st_3.10.0.zip'
Content type 'application/zip' length 38180864 bytes (36.4 MB)
opened URL
downloaded 36.4 MB
The downloaded binary packages are in
C:\Users\msurles\AppData\Local\Temp\RtmpA7V3aP\downloaded_packages
> biocLite("pd.ragene.2.0.st")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.2), R version 3.1.3.
Installing package(s) 'pd.ragene.2.0.st'
trying URL 'http://bioconductor.org/packages/3.0/data/annotation/bin/windows/contrib/3.1/pd.ragene.2.0.st_3.10.0.zip'
Content type 'application/zip' length 38180864 bytes (36.4 MB)
opened URL
downloaded 36.4 MB
> librarypd.ragene.2.0.st)
Loading required package: RSQLite
Loading required package: DBI
Warning message:
package ‘pd.ragene.2.0.st’ was built under R version 3.2.0
> celFiles
[1] "pMCAO_3 hour_IC10_(RaGene-2_0-st).CEL" "pMCAO_3 hour_IC13_(RaGene-2_0-st).CEL" "pMCAO_3 hour_IC15_(RaGene-2_0-st).CEL"
[4] "pMCAO_3 hour_IC19_(RaGene-2_0-st).CEL" "pMCAO_3 hour_IC42_(RaGene-2_0-st).CEL" "pMCAO_3 hour_IC65_(RaGene-2_0-st).CEL"
[7] "pMCAO2015-Sham1_(RaGene-2_0-st).CEL" "pMCAO2015-Sham2_(RaGene-2_0-st).CEL" "pMCAO2015-Sham3_(RaGene-2_0-st).CEL"
[10] "pMCAO2015-Sham4_(RaGene-2_0-st).CEL"
> affyRaw <- read.celfiles(celFiles)
Platform design info loaded.
Reading in : pMCAO_3 hour_IC10_(RaGene-2_0-st).CEL
Reading in : pMCAO_3 hour_IC13_(RaGene-2_0-st).CEL
Reading in : pMCAO_3 hour_IC15_(RaGene-2_0-st).CEL
Reading in : pMCAO_3 hour_IC19_(RaGene-2_0-st).CEL
Reading in : pMCAO_3 hour_IC42_(RaGene-2_0-st).CEL
Reading in : pMCAO_3 hour_IC65_(RaGene-2_0-st).CEL
Reading in : pMCAO2015-Sham1_(RaGene-2_0-st).CEL
Reading in : pMCAO2015-Sham2_(RaGene-2_0-st).CEL
Reading in : pMCAO2015-Sham3_(RaGene-2_0-st).CEL
Reading in : pMCAO2015-Sham4_(RaGene-2_0-st).CEL
> eset <- rma(affyRaw)
Background correcting
Normalizing
Calculating Expression
Warning message:
'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")
