Question: Warning Message-depreciated after running rma in oligo package
0
gravatar for Surles, Monique
4.7 years ago by
United States
Surles, Monique50 wrote:

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 • 1.4k views
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by Surles, Monique50
Answer: Warning Message-depreciated after running rma in oligo package
1
gravatar for Benilton Carvalho
4.7 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.3k wrote:
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 COMMENTlink written 4.7 years ago by Benilton Carvalho4.3k
Answer: Warning Message-depreciated after running rma in oligo package
0
gravatar for Surles, Monique
4.7 years ago by
United States
Surles, Monique50 wrote:

Thank you for the response.

Monique

ADD COMMENTlink written 4.7 years ago by Surles, Monique50
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