Question: justRMA couldn't obtain CDF environment
0
gravatar for Li Liu
5.1 years ago by
Li Liu100
Canada
Li Liu100 wrote:
Dear members, I tried to read a batch of Affymetrix *.cel files and perform normalization using 'justRMA', but I got the following error: Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain OncoScan Library - package oncoscancdf not installed Bioconductor - oncoscancdf not available I couldn't find the package 'oncoscancdf' in Bioconductor. However, when I used the same code run my old '*.cel' files it worked well. Are there anybody who have the experience about this? Many thanks, Li Here are the codes I run and the output: > library(affy) > setwd('U:/li/BR10microarray/data/cel') > eset=justRMA(filenames=list.celfiles(), normalize=T) Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain OncoScan Library - package oncoscancdf not installed Bioconductor - oncoscancdf not available > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help > biocLite('oncoscancdf') BioC_mirror: http://bioconductor.org Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version 3.1.0. Installing package(s) 'oncoscancdf' Warning message: package ‘oncoscancdf’ is not available (for R version 3.1.0) > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-w64-mingw32/x64 (64-bit) 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] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.42.3 Biobase_2.24.0 BiocGenerics_0.10.0 BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] affyio_1.32.0 preprocessCore_1.26.1 tools_3.1.0 zlibbioc_1.10.0 [[alternative HTML version deleted]]
cdf • 1.8k views
ADD COMMENTlink modified 5.1 years ago by James W. MacDonald50k • written 5.1 years ago by Li Liu100
Answer: justRMA couldn't obtain CDF environment
0
gravatar for James W. MacDonald
5.1 years ago by
United States
James W. MacDonald50k wrote:
Hi Li, The affy/makecdfenv pipeline is only intended for use with the 3'-bias expression arrays. The OncoScan arrays are completely different, and won't work with these packages. I don't know if xps or oligo will work with these arrays either; I don't know much about them. However, Affymetrix has their own OncoScan Nexus Express Software that you could use. Best, Jim On 6/26/2014 2:22 PM, Li Liu wrote: > Dear members, > > I tried to read a batch of Affymetrix *.cel files and perform normalization using 'justRMA', but I got the following error: > > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain OncoScan > Library - package oncoscancdf not installed > Bioconductor - oncoscancdf not available > > > I couldn't find the package 'oncoscancdf' in Bioconductor. > > However, when I used the same code run my old '*.cel' files it worked well. Are there anybody who have the experience about this? > > Many thanks, > > Li > > > Here are the codes I run and the output: > >> library(affy) >> setwd('U:/li/BR10microarray/data/cel') >> eset=justRMA(filenames=list.celfiles(), normalize=T) > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain OncoScan > Library - package oncoscancdf not installed > Bioconductor - oncoscancdf not available > > >> source("http://bioconductor.org/biocLite.R") > Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help >> biocLite('oncoscancdf') > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version 3.1.0. > Installing package(s) 'oncoscancdf' > Warning message: > package ?oncoscancdf? is not available (for R version 3.1.0) > >> sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > 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] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] affy_1.42.3 Biobase_2.24.0 BiocGenerics_0.10.0 BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] affyio_1.32.0 preprocessCore_1.26.1 tools_3.1.0 zlibbioc_1.10.0 > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 5.1 years ago by James W. MacDonald50k
Dear Jim and Li, It seems that OncoScan arrays are Genotyping arrays and not expression arrays, see: http://www.affymetrix.com/estore/promotions/mip/index.affx Package xps can only handle expression arrays and thus does not work with OncoScan arrays, but maybe package oligo is able to handle these arrays. Best regards, Christian On 6/26/14 8:49 PM, James W. MacDonald wrote: > Hi Li, > > The affy/makecdfenv pipeline is only intended for use with the 3'-bias > expression arrays. The OncoScan arrays are completely different, and > won't work with these packages. > > I don't know if xps or oligo will work with these arrays either; I don't > know much about them. However, Affymetrix has their own OncoScan Nexus > Express Software that you could use. > > Best, > > Jim > > > > On 6/26/2014 2:22 PM, Li Liu wrote: >> Dear members, >> >> I tried to read a batch of Affymetrix *.cel files and perform >> normalization using 'justRMA', but I got the following error: >> >> Error in getCdfInfo(object) : >> Could not obtain CDF environment, problems encountered: >> Specified environment does not contain OncoScan >> Library - package oncoscancdf not installed >> Bioconductor - oncoscancdf not available >> >> >> I couldn't find the package 'oncoscancdf' in Bioconductor. >> >> However, when I used the same code run my old '*.cel' files it worked >> well. Are there anybody who have the experience about this? >> >> Many thanks, >> >> Li >> >> >> Here are the codes I run and the output: >> >>> library(affy) >>> setwd('U:/li/BR10microarray/data/cel') >>> eset=justRMA(filenames=list.celfiles(), normalize=T) >> Error in getCdfInfo(object) : >> Could not obtain CDF environment, problems encountered: >> Specified environment does not contain OncoScan >> Library - package oncoscancdf not installed >> Bioconductor - oncoscancdf not available >> >> >>> source("http://bioconductor.org/biocLite.R") >> Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help >>> biocLite('oncoscancdf') >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version 3.1.0. >> Installing package(s) 'oncoscancdf' >> Warning message: >> package ?oncoscancdf? is not available (for R version 3.1.0) >> >>> sessionInfo() >> R version 3.1.0 (2014-04-10) >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> >> 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] parallel stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] affy_1.42.3 Biobase_2.24.0 BiocGenerics_0.10.0 >> BiocInstaller_1.14.2 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.32.0 preprocessCore_1.26.1 tools_3.1.0 >> zlibbioc_1.10.0 >> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >
ADD REPLYlink written 5.1 years ago by cstrato3.9k
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