Hi Jim, That has solved the RMA issue. Thank you very much! Any idea for the GCRMA issue? Best, Trent ________________________________________ From: James W. MacDonald [jmacdon@uw.edu] Sent: Monday, June 04, 2012 10:30 AM To: Trent Simmons Cc: bioconductor at r-project.org Subject: Re: [BioC] Unable to perform GCRMA/RMA with cdf file 'mogene11stv1mmentrezgcdf' Hi Trent, On 6/4/2012 10:14 AM, Trent Simmons wrote: > Hi All, > > I am trying to perform a GCRMA normalization of microarray data that was run on Mouse Gene 1.1 Affymetrix arrays. I am running into an issue with the CDF file for that array (the CDF file is mogene11stv1mmentrezgcdf). > > I obtained the latest version of the CDF file from Brainarray. When I attempted to perform the compute.affinities step, the error message: > > .Error in tmp.exprs[pmIndex[subIndex]] = apm : > NAs are not allowed in subscripted assignments > > is returned. Is anyone else experiencing this issue, or have any suggestions for how to resolve it? The default for gcrma() is to use the MM probes to estimate GC- specific background estimates. However, the Gene ST chips are PM-only chips. However, there is an argument to gcrma (NCprobe) that you can use to point to the negative control probes. > > I have also tried to perform basic RMA analysis using one of my CEL files and the same CDF file, just in case it was an issue solely with GCRMA. RMA didn't work either, but in this case, it seems to be that the RMA script is looking for a CDF file called 'mogene11stv1cdf' instead. Once again, anyone else with this issue or suggestions for a fix? See the cdfname argument to ReadAffy. Best, Jim > > > Thanks in advance, > > Trent > > ### START CODE ### > ### LOAD LIBRARIES ### > library(affy) > library(gcrma) > library(AnnotationDbi) > library(mogene11stv1mmentrezgcdf) > library(mogene11stv1mmentrezgprobe) > >> ### RUN GCRMA ### >> compute.affinities('mogene11stv1mmentrezg', verbose = TRUE) > Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : > NAs are not allowed in subscripted assignments >> traceback() > 1: compute.affinities("mogene11stv1mmentrezg", verbose = TRUE) > >> ### RUN RMA ### >> setwd('~/Documents/test/mouse/CEL') >> >> data<- ReadAffy() >> eset<- rma(data) > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain MoGene-1_1-st-v1 > Library - package mogene11stv1cdf not installed > Bioconductor - mogene11stv1cdf not available >> traceback() > 12: stop(paste("Could not obtain CDF environment, problems encountered:", > paste(unlist(badOut), collapse = "\n"), sep = "\n")) > 11: getCdfInfo(object) > 10: .local(object, which, ...) > 9: indexProbes(object, "pm", genenames = genenames) > 8: indexProbes(object, "pm", genenames = genenames) > 7: .local(object, ...) > 6: pmindex(object, genenames) > 5: pmindex(object, genenames) > 4: .local(object, ...) > 3: probeNames(object, subset) > 2: probeNames(object, subset) > 1: rma(data) >> ### SESSION INFO ### >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 > [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] mogene11stv1mmentrezgprobe_15.1.0 mogene11stv1mmentrezgcdf_15.1.0 > [3] AnnotationDbi_1.18.1 gcrma_2.28.0 > [5] BiocInstaller_1.4.6 affy_1.34.0 > [7] Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.24.0 Biostrings_2.24.1 DBI_0.2-5 > [4] IRanges_1.14.3 preprocessCore_1.18.0 RSQLite_0.11.1 > [7] splines_2.15.0 stats4_2.15.0 tools_2.15.0 > [10] zlibbioc_1.2.0 > > ## END CODE ## > _______________________________________________ > 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

Hi Trent, In addition to Jim's comments you also may want to have a look at the suggestions Mike Smith provided some time ago: http://article.gmane.org/gmane.science.biology.informatics.conductor/3 2506 Note: I didn't try it myself, so I cannot comment any further on it. HTH, Guido --------------------------------------------------------- Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld at wur.nl internet: http://nutrigene.4t.com http://scholar.google.com/citations?user=qFHaMnoAAAAJ http://www.researcherid.com/rid/F-4912-2010 -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of James W. MacDonald Sent: Monday, June 04, 2012 16:31 To: Trent Simmons Cc: bioconductor at r-project.org Subject: Re: [BioC] Unable to perform GCRMA/RMA with cdf file 'mogene11stv1mmentrezgcdf' Hi Trent, On 6/4/2012 10:14 AM, Trent Simmons wrote: > Hi All, > > I am trying to perform a GCRMA normalization of microarray data that was run on Mouse Gene 1.1 Affymetrix arrays. I am running into an issue with the CDF file for that array (the CDF file is mogene11stv1mmentrezgcdf). > > I obtained the latest version of the CDF file from Brainarray. When I attempted to perform the compute.affinities step, the error message: > > .Error in tmp.exprs[pmIndex[subIndex]] = apm : > NAs are not allowed in subscripted assignments > > is returned. Is anyone else experiencing this issue, or have any suggestions for how to resolve it? The default for gcrma() is to use the MM probes to estimate GC- specific background estimates. However, the Gene ST chips are PM-only chips. However, there is an argument to gcrma (NCprobe) that you can use to point to the negative control probes. > > I have also tried to perform basic RMA analysis using one of my CEL files and the same CDF file, just in case it was an issue solely with GCRMA. RMA didn't work either, but in this case, it seems to be that the RMA script is looking for a CDF file called 'mogene11stv1cdf' instead. Once again, anyone else with this issue or suggestions for a fix? See the cdfname argument to ReadAffy. Best, Jim > > > Thanks in advance, > > Trent > > ### START CODE ### > ### LOAD LIBRARIES ### > library(affy) > library(gcrma) > library(AnnotationDbi) > library(mogene11stv1mmentrezgcdf) > library(mogene11stv1mmentrezgprobe) > >> ### RUN GCRMA ### >> compute.affinities('mogene11stv1mmentrezg', verbose = TRUE) > Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : > NAs are not allowed in subscripted assignments >> traceback() > 1: compute.affinities("mogene11stv1mmentrezg", verbose = TRUE) > >> ### RUN RMA ### >> setwd('~/Documents/test/mouse/CEL') >> >> data<- ReadAffy() >> eset<- rma(data) > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain MoGene-1_1-st-v1 Library - > package mogene11stv1cdf not installed Bioconductor - mogene11stv1cdf > not available >> traceback() > 12: stop(paste("Could not obtain CDF environment, problems encountered:", > paste(unlist(badOut), collapse = "\n"), sep = "\n")) > 11: getCdfInfo(object) > 10: .local(object, which, ...) > 9: indexProbes(object, "pm", genenames = genenames) > 8: indexProbes(object, "pm", genenames = genenames) > 7: .local(object, ...) > 6: pmindex(object, genenames) > 5: pmindex(object, genenames) > 4: .local(object, ...) > 3: probeNames(object, subset) > 2: probeNames(object, subset) > 1: rma(data) >> ### SESSION INFO ### >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 > [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] mogene11stv1mmentrezgprobe_15.1.0 mogene11stv1mmentrezgcdf_15.1.0 > [3] AnnotationDbi_1.18.1 gcrma_2.28.0 > [5] BiocInstaller_1.4.6 affy_1.34.0 > [7] Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.24.0 Biostrings_2.24.1 DBI_0.2-5 > [4] IRanges_1.14.3 preprocessCore_1.18.0 RSQLite_0.11.1 > [7] splines_2.15.0 stats4_2.15.0 tools_2.15.0 > [10] zlibbioc_1.2.0 > > ## END CODE ## > _______________________________________________ > 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 _______________________________________________ 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

Oh sheesh. I missed the explanation. Sorry, and thank you again! Trent Simmons Volunteer-Student Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Toll-free: 1-866-678-6427 www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. ________________________________________ From: James W. MacDonald [jmacdon@uw.edu] Sent: Monday, June 04, 2012 10:30 AM To: Trent Simmons Cc: bioconductor at r-project.org Subject: Re: [BioC] Unable to perform GCRMA/RMA with cdf file 'mogene11stv1mmentrezgcdf' Hi Trent, On 6/4/2012 10:14 AM, Trent Simmons wrote: > Hi All, > > I am trying to perform a GCRMA normalization of microarray data that was run on Mouse Gene 1.1 Affymetrix arrays. I am running into an issue with the CDF file for that array (the CDF file is mogene11stv1mmentrezgcdf). > > I obtained the latest version of the CDF file from Brainarray. When I attempted to perform the compute.affinities step, the error message: > > .Error in tmp.exprs[pmIndex[subIndex]] = apm : > NAs are not allowed in subscripted assignments > > is returned. Is anyone else experiencing this issue, or have any suggestions for how to resolve it? The default for gcrma() is to use the MM probes to estimate GC- specific background estimates. However, the Gene ST chips are PM-only chips. However, there is an argument to gcrma (NCprobe) that you can use to point to the negative control probes. > > I have also tried to perform basic RMA analysis using one of my CEL files and the same CDF file, just in case it was an issue solely with GCRMA. RMA didn't work either, but in this case, it seems to be that the RMA script is looking for a CDF file called 'mogene11stv1cdf' instead. Once again, anyone else with this issue or suggestions for a fix? See the cdfname argument to ReadAffy. Best, Jim > > > Thanks in advance, > > Trent > > ### START CODE ### > ### LOAD LIBRARIES ### > library(affy) > library(gcrma) > library(AnnotationDbi) > library(mogene11stv1mmentrezgcdf) > library(mogene11stv1mmentrezgprobe) > >> ### RUN GCRMA ### >> compute.affinities('mogene11stv1mmentrezg', verbose = TRUE) > Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm : > NAs are not allowed in subscripted assignments >> traceback() > 1: compute.affinities("mogene11stv1mmentrezg", verbose = TRUE) > >> ### RUN RMA ### >> setwd('~/Documents/test/mouse/CEL') >> >> data<- ReadAffy() >> eset<- rma(data) > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain MoGene-1_1-st-v1 > Library - package mogene11stv1cdf not installed > Bioconductor - mogene11stv1cdf not available >> traceback() > 12: stop(paste("Could not obtain CDF environment, problems encountered:", > paste(unlist(badOut), collapse = "\n"), sep = "\n")) > 11: getCdfInfo(object) > 10: .local(object, which, ...) > 9: indexProbes(object, "pm", genenames = genenames) > 8: indexProbes(object, "pm", genenames = genenames) > 7: .local(object, ...) > 6: pmindex(object, genenames) > 5: pmindex(object, genenames) > 4: .local(object, ...) > 3: probeNames(object, subset) > 2: probeNames(object, subset) > 1: rma(data) >> ### SESSION INFO ### >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 > [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] mogene11stv1mmentrezgprobe_15.1.0 mogene11stv1mmentrezgcdf_15.1.0 > [3] AnnotationDbi_1.18.1 gcrma_2.28.0 > [5] BiocInstaller_1.4.6 affy_1.34.0 > [7] Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.24.0 Biostrings_2.24.1 DBI_0.2-5 > [4] IRanges_1.14.3 preprocessCore_1.18.0 RSQLite_0.11.1 > [7] splines_2.15.0 stats4_2.15.0 tools_2.15.0 > [10] zlibbioc_1.2.0 > > ## END CODE ## > _______________________________________________ > 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