Warning Message-depreciated after running rma in oligo package
2
0
Entering edit mode
@surles-monique-6565
Last seen 9.6 years ago
United States

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") 

oligo pd.ragene.2.0.st • 2.6k views
ADD COMMENT
1
Entering edit mode
@benilton-carvalho-1375
Last seen 4.7 years ago
Brazil/Campinas/UNICAMP
Thank you for the report. This won't affect results and is due to a change in the RSQLite package. A fix is on the way for the next release. By the way, rma() is running just fine for you. The deprecated message is a warning and not an error. b On Tue, Mar 31, 2015 at 8:31 PM Surles, Monique [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Surles, Monique <https: support.bioconductor.org="" u="" 6565=""/> wrote Question: > Warning Message-depreciated after running rma in oligo package > <https: support.bioconductor.org="" p="" 66246=""/>: > > 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") > > > ------------------------------ > > You may reply via email or visit Warning Message-depreciated after running rma in oligo package >
ADD COMMENT
0
Entering edit mode
@surles-monique-6565
Last seen 9.6 years ago
United States

Thank you for the response.

Monique

ADD COMMENT

Login before adding your answer.

Traffic: 428 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6