justRMA?
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@bhargavi-duvvuri-5647
Last seen 9.6 years ago
Hello, I am using justRMA for processing 350 CEL files. When I does with RMA I get 34901 probe intensities which match the CDF file. However, when I run justRMA, I get only 23068 probe intensities. I am not sure why would this happen? Below is the code I am using: library(affy) setwd('/home/run/testcel') expr.vals <- justRMA(cdfname = "primeviewhsrefseqcdf") write.exprs(expr.vals, file= 'Customoutput.csv', sep=",", row.names=F, col.names=T, quote=F) Could you please advise me here on how to modify the script so that I get normalized probe intensities for all the probe sets? Thank you for your attention and time. Bhargavi [[alternative HTML version deleted]]
cdf probe cdf probe • 2.3k views
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@james-w-macdonald-5106
Last seen 7 hours ago
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Hi Bargavi, On 12/7/2012 4:08 PM, Bhargavi Duvvuri wrote: > Hello, > > I am using justRMA for processing 350 CEL files. When I does with RMA I get > 34901 probe intensities which match the CDF file. However, when I run > justRMA, I get only 23068 probe intensities. I am not sure why would this > happen? It shouldn't, and we have done extensive testing to ensure that the results from justRMA() are identical to rma(). As an example: > nrow(exprs(rma(ReadAffy(cdfname = "mogene10stmmrefseqcdf")))) Background correcting Normalizing Calculating Expression [1] 28312 > nrow(exprs(justRMA(cdfname = "mogene10stmmrefseqcdf"))) [1] 28312 So I get the same number of rows using both methods. Now check that I get the same exact values: > all.equal(exprs(rma(ReadAffy(cdfname = "mogene10stmmrefseqcdf"))),exprs(justRMA(cdfname = "mogene10stmmrefseqcdf"))) Background correcting Normalizing Calculating Expression [1] TRUE So it looks OK to me. Best, Jim > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mogene10stmmrefseqcdf_16.0.0 mogene11stmmrefseqcdf_16.0.0 [3] mogene10stv1cdf_2.11.0 AnnotationDbi_1.20.3 [5] affy_1.36.0 Biobase_2.18.0 [7] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 BiocInstaller_1.8.3 DBI_0.2-5 [4] IRanges_1.16.4 parallel_2.15.1 preprocessCore_1.20.0 [7] RSQLite_0.11.2 stats4_2.15.1 tools_2.15.1 [10] zlibbioc_1.4.0 > > > Below is the code I am using: > > library(affy) > setwd('/home/run/testcel') > expr.vals<- justRMA(cdfname = "primeviewhsrefseqcdf") > write.exprs(expr.vals, file= 'Customoutput.csv', sep=",", row.names=F, > col.names=T, quote=F) > > Could you please advise me here on how to modify the script so that I > get normalized probe intensities for all the probe sets? > > Thank you for your attention and time. > > Bhargavi > > [[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
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Hello James, I have tested as you mentioned below: > nrow(exprs(justRMA(cdfname = "PrimeViewHsREFSEQcdf"))) Loading required package: AnnotationDbi [1] 34901 This number is exactly the same as in the CDF file and matches with that of RMA. I get 34901 rows when I process single CEL file. However, when I do justRMA with 350 CEL files, number of rows in the output are 23068. Why would this happen? Please advise. Thank you Bhargavi On Fri, Dec 7, 2012 at 4:42 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Bargavi, > > > On 12/7/2012 4:08 PM, Bhargavi Duvvuri wrote: > >> Hello, >> >> I am using justRMA for processing 350 CEL files. When I does with RMA I >> get >> 34901 probe intensities which match the CDF file. However, when I run >> justRMA, I get only 23068 probe intensities. I am not sure why would this >> happen? >> > > It shouldn't, and we have done extensive testing to ensure that the > results from justRMA() are identical to rma(). As an example: > > > nrow(exprs(rma(ReadAffy(**cdfname = "mogene10stmmrefseqcdf")))) > Background correcting > Normalizing > Calculating Expression > [1] 28312 > > nrow(exprs(justRMA(cdfname = "mogene10stmmrefseqcdf"))) > [1] 28312 > > So I get the same number of rows using both methods. Now check that I get > the same exact values: > > > all.equal(exprs(rma(ReadAffy(**cdfname = "mogene10stmmrefseqcdf"))),**exprs(justRMA(cdfname > = "mogene10stmmrefseqcdf"))) > Background correcting > Normalizing > Calculating Expression > [1] TRUE > > So it looks OK to me. > > Best, > > Jim > > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] mogene10stmmrefseqcdf_16.0.0 mogene11stmmrefseqcdf_16.0.0 > [3] mogene10stv1cdf_2.11.0 AnnotationDbi_1.20.3 > [5] affy_1.36.0 Biobase_2.18.0 > [7] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affyio_1.26.0 BiocInstaller_1.8.3 DBI_0.2-5 > [4] IRanges_1.16.4 parallel_2.15.1 preprocessCore_1.20.0 > [7] RSQLite_0.11.2 stats4_2.15.1 tools_2.15.1 > [10] zlibbioc_1.4.0 > > > > > >> Below is the code I am using: >> >> library(affy) >> setwd('/home/run/testcel') >> expr.vals<- justRMA(cdfname = "primeviewhsrefseqcdf") >> write.exprs(expr.vals, file= 'Customoutput.csv', sep=",", >> row.names=F, >> col.names=T, quote=F) >> >> Could you please advise me here on how to modify the script so that I >> get normalized probe intensities for all the probe sets? >> >> Thank you for your attention and time. >> >> Bhargavi >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<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 > > -- Bhargavi Duvvuri M.Sc, Ph.D TAS/CAN Postdoctoral Research Fellow The Hospital for Sick Children Research Institute Division of Cell Biology MARS Centre - Toronto Medical Discovery Tower 101 College street, Rm 12-401 Bay C Toronto, ON, Canada M5G 1L7 Phone: 416-813-7780 Fax: 416-813-8883 email: bhargavi.duvvuri@sickkids.ca [[alternative HTML version deleted]]
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Hi Bhargavi, On 12/9/2012 1:38 AM, Bhargavi Duvvuri wrote: > Hello James, > > I have tested as you mentioned below: > > > nrow(exprs(justRMA(cdfname = "PrimeViewHsREFSEQcdf"))) > Loading required package: AnnotationDbi > > [1] 34901 > > This number is exactly the same as in the CDF file and matches with > that of RMA. > > I get 34901 rows when I process single CEL file. However, when I do > justRMA with 350 CEL files, number of rows in the output are 23068. > Why would this happen? It shouldn't. I don't have 350 of the same type of celfile to test this with, so I would suggest trying a subset (like 100) and see how that goes. You might be getting an error that you didn't notice. Best, Jim > > Please advise. > > Thank you > > Bhargavi > > On Fri, Dec 7, 2012 at 4:42 PM, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > Hi Bargavi, > > > On 12/7/2012 4:08 PM, Bhargavi Duvvuri wrote: > > Hello, > > I am using justRMA for processing 350 CEL files. When I does > with RMA I get > 34901 probe intensities which match the CDF file. However, > when I run > justRMA, I get only 23068 probe intensities. I am not sure why > would this > happen? > > > It shouldn't, and we have done extensive testing to ensure that > the results from justRMA() are identical to rma(). As an example: > > > nrow(exprs(rma(ReadAffy(cdfname = "mogene10stmmrefseqcdf")))) > Background correcting > Normalizing > Calculating Expression > [1] 28312 > > nrow(exprs(justRMA(cdfname = "mogene10stmmrefseqcdf"))) > [1] 28312 > > So I get the same number of rows using both methods. Now check > that I get the same exact values: > > > all.equal(exprs(rma(ReadAffy(cdfname = > "mogene10stmmrefseqcdf"))),exprs(justRMA(cdfname = > "mogene10stmmrefseqcdf"))) > Background correcting > Normalizing > Calculating Expression > [1] TRUE > > So it looks OK to me. > > Best, > > Jim > > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] mogene10stmmrefseqcdf_16.0.0 mogene11stmmrefseqcdf_16.0.0 > [3] mogene10stv1cdf_2.11.0 AnnotationDbi_1.20.3 > [5] affy_1.36.0 Biobase_2.18.0 > [7] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affyio_1.26.0 BiocInstaller_1.8.3 DBI_0.2-5 > [4] IRanges_1.16.4 parallel_2.15.1 preprocessCore_1.20.0 > [7] RSQLite_0.11.2 stats4_2.15.1 tools_2.15.1 > [10] zlibbioc_1.4.0 > > > > > > Below is the code I am using: > > library(affy) > setwd('/home/run/testcel') > expr.vals<- justRMA(cdfname = "primeviewhsrefseqcdf") > write.exprs(expr.vals, file= 'Customoutput.csv', sep=",", > row.names=F, > col.names=T, quote=F) > > Could you please advise me here on how to modify the script so > that I > get normalized probe intensities for all the probe sets? > > Thank you for your attention and time. > > Bhargavi > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto: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 > > > > > -- > Bhargavi Duvvuri M.Sc, Ph.D > TAS/CAN Postdoctoral Research Fellow > The Hospital for Sick Children Research Institute > Division of Cell Biology > MARS Centre - Toronto Medical Discovery Tower > 101 College street, Rm 12-401 Bay C > Toronto, ON, Canada M5G 1L7 > Phone: 416-813-7780 > Fax: 416-813-8883 > email: bhargavi.duvvuri at sickkids.ca <mailto:bhargavi.duvvuri at="" sickkids.ca=""> > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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@james-w-macdonald-5106
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Hi Bhargavi, Please don't take things off-list. On 12/11/2012 12:05 PM, Bhargavi Duvvuri wrote: > Hello James, > > Thank you for your reply. > > Here is the new issue I get with RMA: > > When I run on Windows operating system I get 34901 probe intensities > with one or many CEL files. Same output with justRMA, as you said. > > However, when I run same on Mac OS and Linux, I would get 23068 probe > intensities with one or many CEL files. Same output with justRMA. > > Same version of R and affy on three operating systems. What is your output from sessionInfo() on Linux? Make sure you have loaded the primeviewhsrefseqcdf package first. Also, what do you get from length(ls(primeviewhsrefseqcdf)) on Linux? Best, Jim > > Why would this happen? I can run batch of CEL files only on Mac or > Linux due to memory issues. > > Could you please advise? > > Thank you > > Bhargavi > > > > On Mon, Dec 10, 2012 at 9:26 AM, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > Hi Bhargavi, > > > On 12/9/2012 1:38 AM, Bhargavi Duvvuri wrote: > > Hello James, > > I have tested as you mentioned below: > > > nrow(exprs(justRMA(cdfname = "PrimeViewHsREFSEQcdf"))) > Loading required package: AnnotationDbi > > [1] 34901 > > This number is exactly the same as in the CDF file and matches > with that of RMA. > > I get 34901 rows when I process single CEL file. However, > when I do justRMA with 350 CEL files, number of rows in the > output are 23068. Why would this happen? > > > It shouldn't. I don't have 350 of the same type of celfile to test > this with, so I would suggest trying a subset (like 100) and see > how that goes. You might be getting an error that you didn't notice. > > Best, > > Jim > > > > Please advise. > > Thank you > > Bhargavi > > On Fri, Dec 7, 2012 at 4:42 PM, James W. MacDonald > <jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu=""> <mailto:jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">>> wrote: > > Hi Bargavi, > > > On 12/7/2012 4:08 PM, Bhargavi Duvvuri wrote: > > Hello, > > I am using justRMA for processing 350 CEL files. When > I does > with RMA I get > 34901 probe intensities which match the CDF file. > However, > when I run > justRMA, I get only 23068 probe intensities. I am not > sure why > would this > happen? > > > It shouldn't, and we have done extensive testing to ensure > that > the results from justRMA() are identical to rma(). As an > example: > > > nrow(exprs(rma(ReadAffy(cdfname = "mogene10stmmrefseqcdf")))) > Background correcting > Normalizing > Calculating Expression > [1] 28312 > > nrow(exprs(justRMA(cdfname = "mogene10stmmrefseqcdf"))) > [1] 28312 > > So I get the same number of rows using both methods. Now check > that I get the same exact values: > > > all.equal(exprs(rma(ReadAffy(cdfname = > "mogene10stmmrefseqcdf"))),exprs(justRMA(cdfname = > "mogene10stmmrefseqcdf"))) > Background correcting > Normalizing > Calculating Expression > [1] TRUE > > So it looks OK to me. > > Best, > > Jim > > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] mogene10stmmrefseqcdf_16.0.0 mogene11stmmrefseqcdf_16.0.0 > [3] mogene10stv1cdf_2.11.0 AnnotationDbi_1.20.3 > [5] affy_1.36.0 Biobase_2.18.0 > [7] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affyio_1.26.0 BiocInstaller_1.8.3 DBI_0.2-5 > [4] IRanges_1.16.4 parallel_2.15.1 > preprocessCore_1.20.0 > [7] RSQLite_0.11.2 stats4_2.15.1 tools_2.15.1 > [10] zlibbioc_1.4.0 > > > > > > Below is the code I am using: > > library(affy) > setwd('/home/run/testcel') > expr.vals<- justRMA(cdfname = "primeviewhsrefseqcdf") > write.exprs(expr.vals, file= 'Customoutput.csv', > sep=",", > row.names=F, > col.names=T, quote=F) > > Could you please advise me here on how to modify the > script so > that I > get normalized probe intensities for all the probe sets? > > Thank you for your attention and time. > > Bhargavi > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto:bioconductor at="" r-project.org=""> <mailto: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 > > > > > -- > Bhargavi Duvvuri M.Sc, Ph.D > TAS/CAN Postdoctoral Research Fellow > The Hospital for Sick Children Research Institute > Division of Cell Biology > MARS Centre - Toronto Medical Discovery Tower > 101 College street, Rm 12-401 Bay C > Toronto, ON, Canada M5G 1L7 > Phone: 416-813-7780 <tel:416-813-7780> > Fax: 416-813-8883 <tel:416-813-8883> > email: bhargavi.duvvuri at sickkids.ca > <mailto:bhargavi.duvvuri at="" sickkids.ca=""> > <mailto:bhargavi.duvvuri at="" sickkids.ca=""> <mailto:bhargavi.duvvuri at="" sickkids.ca="">> > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > > > -- > Bhargavi Duvvuri M.Sc, Ph.D > TAS/CAN Postdoctoral Research Fellow > The Hospital for Sick Children Research Institute > Division of Cell Biology > MARS Centre - Toronto Medical Discovery Tower > 101 College street, Rm 12-401 Bay C > Toronto, ON, Canada M5G 1L7 > Phone: 416-813-7780 > Fax: 416-813-8883 > email: bhargavi.duvvuri at sickkids.ca <mailto:bhargavi.duvvuri at="" sickkids.ca=""> > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hello James, Here is the session info after I run justRMA. R version 2.15.0 (2012-03-30) Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [Previously saved workspace restored] > library(affy) Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following object(s) are masked from 'package:stats': xtabs The following object(s) are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, cbind, colnames, duplicated, eval, get, intersect, lapply, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, rownames, sapply, setdiff, table, tapply, union, unique 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")'. > setwd('/home/run/testcel') > expr.vals <- justRMA(cdfname = "PrimeViewHsREFSEQcdf") Loading required package: AnnotationDbi > write.exprs(expr.vals, file= 'Customoutput.csv', sep=",", row.names=F, col.names=T, quote=F) > > proc.time() user system elapsed 399.416 21.025 440.413 With length(ls(**primeviewhsrefseqcdf)) I get: length(ls(primeviewhsrefseqcdf)) [1] 20367 Thank you On Tue, Dec 11, 2012 at 12:44 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Bhargavi, > > Please don't take things off-list. > > > On 12/11/2012 12:05 PM, Bhargavi Duvvuri wrote: > >> Hello James, >> >> Thank you for your reply. >> >> Here is the new issue I get with RMA: >> >> When I run on Windows operating system I get 34901 probe intensities with >> one or many CEL files. Same output with justRMA, as you said. >> >> However, when I run same on Mac OS and Linux, I would get 23068 probe >> intensities with one or many CEL files. Same output with justRMA. >> >> Same version of R and affy on three operating systems. >> > > What is your output from sessionInfo() on Linux? Make sure you have loaded > the primeviewhsrefseqcdf package first. > > Also, what do you get from > > length(ls(**primeviewhsrefseqcdf)) > > on Linux? > > Best, > > Jim > > > >> Why would this happen? I can run batch of CEL files only on Mac or Linux >> due to memory issues. >> >> Could you please advise? >> >> Thank you >> >> Bhargavi >> >> >> >> On Mon, Dec 10, 2012 at 9:26 AM, James W. MacDonald <jmacdon@uw.edu<mailto:>> jmacdon@uw.edu>> wrote: >> >> Hi Bhargavi, >> >> >> On 12/9/2012 1:38 AM, Bhargavi Duvvuri wrote: >> >> Hello James, >> >> I have tested as you mentioned below: >> >> > nrow(exprs(justRMA(cdfname = "PrimeViewHsREFSEQcdf"))) >> Loading required package: AnnotationDbi >> >> [1] 34901 >> >> This number is exactly the same as in the CDF file and matches >> with that of RMA. >> >> I get 34901 rows when I process single CEL file. However, >> when I do justRMA with 350 CEL files, number of rows in the >> output are 23068. Why would this happen? >> >> >> It shouldn't. I don't have 350 of the same type of celfile to test >> this with, so I would suggest trying a subset (like 100) and see >> how that goes. You might be getting an error that you didn't notice. >> >> Best, >> >> Jim >> >> >> >> Please advise. >> >> Thank you >> >> Bhargavi >> >> On Fri, Dec 7, 2012 at 4:42 PM, James W. MacDonald >> <jmacdon@uw.edu <mailto:jmacdon@uw.edu=""> <mailto:jmacdon@uw.edu>> >> <mailto:jmacdon@uw.edu>>> wrote: >> >> Hi Bargavi, >> >> >> On 12/7/2012 4:08 PM, Bhargavi Duvvuri wrote: >> >> Hello, >> >> I am using justRMA for processing 350 CEL files. When >> I does >> with RMA I get >> 34901 probe intensities which match the CDF file. >> However, >> when I run >> justRMA, I get only 23068 probe intensities. I am not >> sure why >> would this >> happen? >> >> >> It shouldn't, and we have done extensive testing to ensure >> that >> the results from justRMA() are identical to rma(). As an >> example: >> >> > nrow(exprs(rma(ReadAffy(**cdfname = "mogene10stmmrefseqcdf")))) >> Background correcting >> Normalizing >> Calculating Expression >> [1] 28312 >> > nrow(exprs(justRMA(cdfname = "mogene10stmmrefseqcdf"))) >> [1] 28312 >> >> So I get the same number of rows using both methods. Now check >> that I get the same exact values: >> >> > all.equal(exprs(rma(ReadAffy(**cdfname = >> "mogene10stmmrefseqcdf"))),**exprs(justRMA(cdfname = >> "mogene10stmmrefseqcdf"))) >> Background correcting >> Normalizing >> Calculating Expression >> [1] TRUE >> >> So it looks OK to me. >> >> Best, >> >> Jim >> >> > sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] mogene10stmmrefseqcdf_16.0.0 mogene11stmmrefseqcdf_16.0.0 >> [3] mogene10stv1cdf_2.11.0 AnnotationDbi_1.20.3 >> [5] affy_1.36.0 Biobase_2.18.0 >> [7] BiocGenerics_0.4.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.26.0 BiocInstaller_1.8.3 DBI_0.2-5 >> [4] IRanges_1.16.4 parallel_2.15.1 >> preprocessCore_1.20.0 >> [7] RSQLite_0.11.2 stats4_2.15.1 tools_2.15.1 >> [10] zlibbioc_1.4.0 >> > >> >> >> >> Below is the code I am using: >> >> library(affy) >> setwd('/home/run/testcel') >> expr.vals<- justRMA(cdfname = "primeviewhsrefseqcdf") >> write.exprs(expr.vals, file= 'Customoutput.csv', >> sep=",", >> row.names=F, >> col.names=T, quote=F) >> >> Could you please advise me here on how to modify the >> script so >> that I >> get normalized probe intensities for all the probe sets? >> >> Thank you for your attention and time. >> >> Bhargavi >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> <mailto:bioconductor@r-**project.org <bioconductor@r-project.org=""> >> >> <mailto:bioconductor@r-**project.org <bioconductor@r-project.org=""> >> >> >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: >> http://news.gmane.org/gmane.**science.biology.informatics.** >> conductor<http: news.gmane.org="" gmane.science.biology.informatics.c="" onductor=""> >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> >> >> >> -- Bhargavi Duvvuri M.Sc, Ph.D >> TAS/CAN Postdoctoral Research Fellow >> The Hospital for Sick Children Research Institute >> Division of Cell Biology >> MARS Centre - Toronto Medical Discovery Tower >> 101 College street, Rm 12-401 Bay C >> Toronto, ON, Canada M5G 1L7 >> Phone: 416-813-7780 <tel:416-813-7780> >> Fax: 416-813-8883 <tel:416-813-8883> >> email: bhargavi.duvvuri@sickkids.ca >> <mailto:bhargavi.duvvuri@**sickkids.ca<bhargavi.duvvuri@sickkids.ca> >> > >> <mailto:bhargavi.duvvuri@**sickkids.ca<bhargavi.duvvuri@sickkids.ca> >> >> <mailto:bhargavi.duvvuri@**sickkids.ca<bhargavi.duvvuri@sickkids.ca> >> >> >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> >> >> >> -- >> Bhargavi Duvvuri M.Sc, Ph.D >> TAS/CAN Postdoctoral Research Fellow >> The Hospital for Sick Children Research Institute >> Division of Cell Biology >> MARS Centre - Toronto Medical Discovery Tower >> 101 College street, Rm 12-401 Bay C >> Toronto, ON, Canada M5G 1L7 >> Phone: 416-813-7780 >> Fax: 416-813-8883 >> email: bhargavi.duvvuri@sickkids.ca <mailto:bhargavi.duvvuri@**>> sickkids.ca <bhargavi.duvvuri@sickkids.ca>> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- Bhargavi Duvvuri M.Sc, Ph.D TAS/CAN Postdoctoral Research Fellow The Hospital for Sick Children Research Institute Division of Cell Biology MARS Centre - Toronto Medical Discovery Tower 101 College street, Rm 12-401 Bay C Toronto, ON, Canada M5G 1L7 Phone: 416-813-7780 Fax: 416-813-8883 email: bhargavi.duvvuri@sickkids.ca [[alternative HTML version deleted]]
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Hi Bhargavi, By sessionInfo(), I meant for you to type sessionInfo() at an R prompt, which will say which version of packages you have. Anyway, the problem lies with the primeviewhsrefseqcdf package you are using. When you run length(ls(primeviewhsrefseqcdf)) it tells you how many probesets that cdf package recognizes, and that is why you get a different number on Linux. If I do the same on Windows I get this: > length(ls(primeviewhsrefseqcdf)) [1] 34901 And then if I do that on Linux, I get > length(ls(primeviewhsrefseqcdf)) [1] 34901 Which obviously agrees. Then if I show my sessionInfo(), you can see the versions I am using and what you need to upgrade to. > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] primeviewhsrefseqcdf_16.0.0 AnnotationDbi_1.20.3 [3] Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] DBI_0.2-5 IRanges_1.16.4 parallel_2.15.1 RSQLite_0.11.2 [5] stats4_2.15.1 tools_2.15.1 Best, Jim On 12/11/2012 3:09 PM, Bhargavi Duvvuri wrote: > Hello James, > > Here is the session info after I run justRMA. > > R version 2.15.0 (2012-03-30) > Copyright (C) 2012 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-unknown-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > [Previously saved workspace restored] > > > library(affy) > Loading required package: BiocGenerics > > Attaching package: 'BiocGenerics' > > The following object(s) are masked from 'package:stats': > > xtabs > > The following object(s) are masked from 'package:base': > > Filter, Find, Map, Position, Reduce, anyDuplicated, cbind, > colnames, duplicated, eval, get, intersect, lapply, mapply, mget, > order, paste, pmax, pmax.int <http: pmax.int="">, pmin, pmin.int > <http: pmin.int="">, rbind, rep.int <http: rep.int="">, > rownames, sapply, setdiff, table, tapply, union, unique > > 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")'. > > > setwd('/home/run/testcel') > > expr.vals <- justRMA(cdfname = "PrimeViewHsREFSEQcdf") > Loading required package: AnnotationDbi > > > write.exprs(expr.vals, file= 'Customoutput.csv', sep=",", > row.names=F, col.names=T, quote=F) > > > > proc.time() > user system elapsed > 399.416 21.025 440.413 > > With length(ls(primeviewhsrefseqcdf)) I get: > > length(ls(primeviewhsrefseqcdf)) > [1] 20367 > > > Thank you > > On Tue, Dec 11, 2012 at 12:44 PM, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > Hi Bhargavi, > > Please don't take things off-list. > > > On 12/11/2012 12:05 PM, Bhargavi Duvvuri wrote: > > Hello James, > > Thank you for your reply. > > Here is the new issue I get with RMA: > > When I run on Windows operating system I get 34901 probe > intensities with one or many CEL files. Same output with > justRMA, as you said. > > However, when I run same on Mac OS and Linux, I would get > 23068 probe intensities with one or many CEL files. Same > output with justRMA. > > Same version of R and affy on three operating systems. > > > What is your output from sessionInfo() on Linux? Make sure you > have loaded the primeviewhsrefseqcdf package first. > > Also, what do you get from > > length(ls(primeviewhsrefseqcdf)) > > on Linux? > > Best, > > Jim > > > > Why would this happen? I can run batch of CEL files only on > Mac or Linux due to memory issues. > > Could you please advise? > > Thank you > > Bhargavi > > > > On Mon, Dec 10, 2012 at 9:26 AM, James W. MacDonald > <jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu=""> <mailto:jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">>> wrote: > > Hi Bhargavi, > > > On 12/9/2012 1:38 AM, Bhargavi Duvvuri wrote: > > Hello James, > > I have tested as you mentioned below: > > > nrow(exprs(justRMA(cdfname = "PrimeViewHsREFSEQcdf"))) > Loading required package: AnnotationDbi > > [1] 34901 > > This number is exactly the same as in the CDF file and > matches > with that of RMA. > > I get 34901 rows when I process single CEL file. However, > when I do justRMA with 350 CEL files, number of rows > in the > output are 23068. Why would this happen? > > > It shouldn't. I don't have 350 of the same type of celfile > to test > this with, so I would suggest trying a subset (like 100) > and see > how that goes. You might be getting an error that you > didn't notice. > > Best, > > Jim > > > > Please advise. > > Thank you > > Bhargavi > > On Fri, Dec 7, 2012 at 4:42 PM, James W. MacDonald > <jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu=""> <mailto:jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> <mailto:jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu=""> > > <mailto:jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu="">>>> wrote: > > Hi Bargavi, > > > On 12/7/2012 4:08 PM, Bhargavi Duvvuri wrote: > > Hello, > > I am using justRMA for processing 350 CEL > files. When > I does > with RMA I get > 34901 probe intensities which match the CDF file. > However, > when I run > justRMA, I get only 23068 probe intensities. I > am not > sure why > would this > happen? > > > It shouldn't, and we have done extensive testing > to ensure > that > the results from justRMA() are identical to rma(). > As an > example: > > > nrow(exprs(rma(ReadAffy(cdfname = "mogene10stmmrefseqcdf")))) > Background correcting > Normalizing > Calculating Expression > [1] 28312 > > nrow(exprs(justRMA(cdfname = "mogene10stmmrefseqcdf"))) > [1] 28312 > > So I get the same number of rows using both > methods. Now check > that I get the same exact values: > > > all.equal(exprs(rma(ReadAffy(cdfname = > "mogene10stmmrefseqcdf"))),exprs(justRMA(cdfname = > "mogene10stmmrefseqcdf"))) > Background correcting > Normalizing > Calculating Expression > [1] TRUE > > So it looks OK to me. > > Best, > > Jim > > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 > LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] mogene10stmmrefseqcdf_16.0.0 > mogene11stmmrefseqcdf_16.0.0 > [3] mogene10stv1cdf_2.11.0 AnnotationDbi_1.20.3 > [5] affy_1.36.0 Biobase_2.18.0 > [7] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affyio_1.26.0 BiocInstaller_1.8.3 > DBI_0.2-5 > [4] IRanges_1.16.4 parallel_2.15.1 > preprocessCore_1.20.0 > [7] RSQLite_0.11.2 stats4_2.15.1 > tools_2.15.1 > [10] zlibbioc_1.4.0 > > > > > > Below is the code I am using: > > library(affy) > setwd('/home/run/testcel') > expr.vals<- justRMA(cdfname = > "primeviewhsrefseqcdf") > write.exprs(expr.vals, file= > 'Customoutput.csv', > sep=",", > row.names=F, > col.names=T, quote=F) > > Could you please advise me here on how to > modify the > script so > that I > get normalized probe intensities for all the > probe sets? > > Thank you for your attention and time. > > Bhargavi > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto:bioconductor at="" r-project.org=""> <mailto:bioconductor at="" r-project.org="">> > <mailto:bioconductor at="" r-project.org=""> <mailto:bioconductor at="" r-project.org=""> > > <mailto:bioconductor at="" r-project.org=""> <mailto: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 > > > > > -- Bhargavi Duvvuri M.Sc, Ph.D > TAS/CAN Postdoctoral Research Fellow > The Hospital for Sick Children Research Institute > Division of Cell Biology > MARS Centre - Toronto Medical Discovery Tower > 101 College street, Rm 12-401 Bay C > Toronto, ON, Canada M5G 1L7 > Phone: 416-813-7780 <tel:416-813-7780> > <tel:416-813-7780 <tel:416-813-7780="">> > Fax: 416-813-8883 <tel:416-813-8883> <tel:416-813-8883> <tel:416-813-8883>> > email: bhargavi.duvvuri at sickkids.ca > <mailto:bhargavi.duvvuri at="" sickkids.ca=""> > <mailto:bhargavi.duvvuri at="" sickkids.ca=""> <mailto:bhargavi.duvvuri at="" sickkids.ca="">> > <mailto:bhargavi.duvvuri at="" sickkids.ca=""> <mailto:bhargavi.duvvuri at="" sickkids.ca=""> > > <mailto:bhargavi.duvvuri at="" sickkids.ca=""> <mailto:bhargavi.duvvuri at="" sickkids.ca="">>> > > > -- James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > > > -- > Bhargavi Duvvuri M.Sc, Ph.D > TAS/CAN Postdoctoral Research Fellow > The Hospital for Sick Children Research Institute > Division of Cell Biology > MARS Centre - Toronto Medical Discovery Tower > 101 College street, Rm 12-401 Bay C > Toronto, ON, Canada M5G 1L7 > Phone: 416-813-7780 <tel:416-813-7780> > Fax: 416-813-8883 <tel:416-813-8883> > email: bhargavi.duvvuri at sickkids.ca > <mailto:bhargavi.duvvuri at="" sickkids.ca=""> > <mailto:bhargavi.duvvuri at="" sickkids.ca=""> <mailto:bhargavi.duvvuri at="" sickkids.ca="">> > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > > > -- > Bhargavi Duvvuri M.Sc, Ph.D > TAS/CAN Postdoctoral Research Fellow > The Hospital for Sick Children Research Institute > Division of Cell Biology > MARS Centre - Toronto Medical Discovery Tower > 101 College street, Rm 12-401 Bay C > Toronto, ON, Canada M5G 1L7 > Phone: 416-813-7780 > Fax: 416-813-8883 > email: bhargavi.duvvuri at sickkids.ca <mailto:bhargavi.duvvuri at="" sickkids.ca=""> > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hello James, I am very new to R. I see minor change in the R version. My version of R sessionInfo() *R version 2.15.0 (2012-03-30)* Platform: x86_64-unknown-linux-gnu (64-bit) loaded via a namespace (and not attached): [1] DBI_0.2-5 IRanges_1.16.4 parallel_2.15.0 RSQLite_0.11.2 [5] stats4_2.15.0 tools_2.15.0 Your version of sessionInfo(): *R version 2.15.1 (2012-06-22)* Platform: x86_64-unknown-linux-gnu (64-bit) other attached packages: loaded via a namespace (and not attached): [1] DBI_0.2-5 IRanges_1.16.4 parallel_2.15.1 RSQLite_0.11.2 [5] stats4_2.15.1 tools_2.15.1 Do you think this minor difference would make effect? Thank you Bhargavi On Tue, Dec 11, 2012 at 3:18 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > R version 2.15.1 (2012-06-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > -- Bhargavi Duvvuri M.Sc, Ph.D TAS/CAN Postdoctoral Research Fellow The Hospital for Sick Children Research Institute Division of Cell Biology MARS Centre - Toronto Medical Discovery Tower 101 College street, Rm 12-401 Bay C Toronto, ON, Canada M5G 1L7 Phone: 416-813-7780 Fax: 416-813-8883 email: bhargavi.duvvuri@sickkids.ca [[alternative HTML version deleted]]
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On 12/11/2012 3:53 PM, Bhargavi Duvvuri wrote: > Hello James, > > I am very new to R. > > I see minor change in the R version. > > My version of R sessionInfo() > > *R version 2.15.0 (2012-03-30)* > Platform: x86_64-unknown-linux-gnu (64-bit) > loaded via a namespace (and not attached): > [1] DBI_0.2-5 IRanges_1.16.4 parallel_2.15.0 RSQLite_0.11.2 > [5] stats4_2.15.0 tools_2.15.0 > > Your version of sessionInfo(): > > *R version 2.15.1 (2012-06-22)* > Platform: x86_64-unknown-linux-gnu (64-bit) > other attached packages: > > loaded via a namespace (and not attached): > [1] DBI_0.2-5 IRanges_1.16.4 parallel_2.15.1 RSQLite_0.11.2 > [5] stats4_2.15.1 tools_2.15.1 > > Do you think this minor difference would make effect? No. But if you re-read what I have said below, you will note I am not talking about the version of R you are using. Instead, I am talking about the version of primeviewhsrefseqcdf you are using. The package you are using is different from the one I am using, and since you didn't load it before running sessionInfo() I have no idea what you are using. If the version is the same as mine, then I would assume there was a problem somewhere along the line and you need to re-install. Well, actually I think you need to re-install regardless. So try that and see if the updated version of that package looks OK. Best, Jim > > Thank you > > Bhargavi > > > On Tue, Dec 11, 2012 at 3:18 PM, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > R version 2.15.1 (2012-06-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > > > > -- > Bhargavi Duvvuri M.Sc, Ph.D > TAS/CAN Postdoctoral Research Fellow > The Hospital for Sick Children Research Institute > Division of Cell Biology > MARS Centre - Toronto Medical Discovery Tower > 101 College street, Rm 12-401 Bay C > Toronto, ON, Canada M5G 1L7 > Phone: 416-813-7780 > Fax: 416-813-8883 > email: bhargavi.duvvuri at sickkids.ca <mailto:bhargavi.duvvuri at="" sickkids.ca=""> > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hello James, The one I am using: [1]* primeviewhsrefseqcdf_1.36.0* AnnotationDbi_1.20.3 [3] Biobase_2.18.0 BiocGenerics_0.4.0 Your primeview package *primeviewhsrefseqcdf_16.0.0* * * My windows version: *PrimeViewHsREFSEQcdf_1.36.0 * * * As you ca see windows and Linux versions I am using are the same, except for uppercase and lowercase. On windows I get 34901 and on Linux i get 26308 *. *If it was for the primeview package version, why would this work on windows? Please advise. Thank you * * *Bhargavi* On Tue, Dec 11, 2012 at 3:58 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > > > On 12/11/2012 3:53 PM, Bhargavi Duvvuri wrote: > >> Hello James, >> >> I am very new to R. >> >> I see minor change in the R version. >> >> My version of R sessionInfo() >> >> *R version 2.15.0 (2012-03-30)* >> >> Platform: x86_64-unknown-linux-gnu (64-bit) >> loaded via a namespace (and not attached): >> [1] DBI_0.2-5 IRanges_1.16.4 parallel_2.15.0 RSQLite_0.11.2 >> [5] stats4_2.15.0 tools_2.15.0 >> >> Your version of sessionInfo(): >> >> *R version 2.15.1 (2012-06-22)* >> >> Platform: x86_64-unknown-linux-gnu (64-bit) >> other attached packages: >> >> loaded via a namespace (and not attached): >> [1] DBI_0.2-5 IRanges_1.16.4 parallel_2.15.1 RSQLite_0.11.2 >> [5] stats4_2.15.1 tools_2.15.1 >> >> Do you think this minor difference would make effect? >> > > No. But if you re-read what I have said below, you will note I am not > talking about the version of R you are using. Instead, I am talking about > the version of primeviewhsrefseqcdf you are using. > > The package you are using is different from the one I am using, and since > you didn't load it before running sessionInfo() I have no idea what you are > using. If the version is the same as mine, then I would assume there was a > problem somewhere along the line and you need to re-install. Well, actually > I think you need to re-install regardless. > > So try that and see if the updated version of that package looks OK. > > Best, > > Jim > > >> Thank you >> >> Bhargavi >> >> >> >> On Tue, Dec 11, 2012 at 3:18 PM, James W. MacDonald <jmacdon@uw.edu<mailto:>> jmacdon@uw.edu>> wrote: >> >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> >> >> >> -- >> Bhargavi Duvvuri M.Sc, Ph.D >> TAS/CAN Postdoctoral Research Fellow >> The Hospital for Sick Children Research Institute >> Division of Cell Biology >> MARS Centre - Toronto Medical Discovery Tower >> 101 College street, Rm 12-401 Bay C >> Toronto, ON, Canada M5G 1L7 >> Phone: 416-813-7780 >> Fax: 416-813-8883 >> email: bhargavi.duvvuri@sickkids.ca <mailto:bhargavi.duvvuri@**>> sickkids.ca <bhargavi.duvvuri@sickkids.ca>> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- Bhargavi Duvvuri M.Sc, Ph.D TAS/CAN Postdoctoral Research Fellow The Hospital for Sick Children Research Institute Division of Cell Biology MARS Centre - Toronto Medical Discovery Tower 101 College street, Rm 12-401 Bay C Toronto, ON, Canada M5G 1L7 Phone: 416-813-7780 Fax: 416-813-8883 email: bhargavi.duvvuri@sickkids.ca [[alternative HTML version deleted]]
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Hi Bhargavi, On 12/11/2012 4:14 PM, Bhargavi Duvvuri wrote: > Hello James, > > The one I am using: > > [1]*primeviewhsrefseqcdf_1.36.0* AnnotationDbi_1.20.3 > [3] Biobase_2.18.0 BiocGenerics_0.4.0 > > > Your primeview package > *primeviewhsrefseqcdf_16.0.0* > * > * > My windows version: > *PrimeViewHsREFSEQcdf_1.36.0 * > * > * > As you ca see windows and Linux versions I am using are the same, > except for uppercase and lowercase. On windows I get 34901 and on > Linux i get 26308*. *If it was for the primeview package version, why > would this work on windows? > > Please advise. I have been trying to advise, but you seem intent on not being advised. So this is my last shot. Expect no more responses from me on this subject. TYPE EXACTLY WHAT I HAVE WRITTEN BELOW AT AN R PROMPT ON YOUR LINUX BOX. library(BiocInstaller) biocLite("primeviewhsrefseqcdf") > > Thank you > * > * > *Bhargavi* > > > On Tue, Dec 11, 2012 at 3:58 PM, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > > > On 12/11/2012 3:53 PM, Bhargavi Duvvuri wrote: > > Hello James, > > I am very new to R. > > I see minor change in the R version. > > My version of R sessionInfo() > > *R version 2.15.0 (2012-03-30)* > > Platform: x86_64-unknown-linux-gnu (64-bit) > loaded via a namespace (and not attached): > [1] DBI_0.2-5 IRanges_1.16.4 parallel_2.15.0 RSQLite_0.11.2 > [5] stats4_2.15.0 tools_2.15.0 > > Your version of sessionInfo(): > > *R version 2.15.1 (2012-06-22)* > > Platform: x86_64-unknown-linux-gnu (64-bit) > other attached packages: > > loaded via a namespace (and not attached): > [1] DBI_0.2-5 IRanges_1.16.4 parallel_2.15.1 RSQLite_0.11.2 > [5] stats4_2.15.1 tools_2.15.1 > > Do you think this minor difference would make effect? > > > No. But if you re-read what I have said below, you will note I am > not talking about the version of R you are using. Instead, I am > talking about the version of primeviewhsrefseqcdf you are using. > > The package you are using is different from the one I am using, > and since you didn't load it before running sessionInfo() I have > no idea what you are using. If the version is the same as mine, > then I would assume there was a problem somewhere along the line > and you need to re-install. Well, actually I think you need to > re-install regardless. > > So try that and see if the updated version of that package looks OK. > > Best, > > Jim > > > Thank you > > Bhargavi > > > > On Tue, Dec 11, 2012 at 3:18 PM, James W. MacDonald > <jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu=""> <mailto:jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">>> wrote: > > R version 2.15.1 (2012-06-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > > > > -- > Bhargavi Duvvuri M.Sc, Ph.D > TAS/CAN Postdoctoral Research Fellow > The Hospital for Sick Children Research Institute > Division of Cell Biology > MARS Centre - Toronto Medical Discovery Tower > 101 College street, Rm 12-401 Bay C > Toronto, ON, Canada M5G 1L7 > Phone: 416-813-7780 <tel:416-813-7780> > Fax: 416-813-8883 <tel:416-813-8883> > email: bhargavi.duvvuri at sickkids.ca > <mailto:bhargavi.duvvuri at="" sickkids.ca=""> > <mailto:bhargavi.duvvuri at="" sickkids.ca=""> <mailto:bhargavi.duvvuri at="" sickkids.ca="">> > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > > > -- > Bhargavi Duvvuri M.Sc, Ph.D > TAS/CAN Postdoctoral Research Fellow > The Hospital for Sick Children Research Institute > Division of Cell Biology > MARS Centre - Toronto Medical Discovery Tower > 101 College street, Rm 12-401 Bay C > Toronto, ON, Canada M5G 1L7 > Phone: 416-813-7780 > Fax: 416-813-8883 > email: bhargavi.duvvuri at sickkids.ca <mailto:bhargavi.duvvuri at="" sickkids.ca=""> > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Thank you again, James. This confusion is because of myself being new to R. Hope you understand this. Regards, Bhargavi On Tue, Dec 11, 2012 at 4:25 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Bhargavi, > > > On 12/11/2012 4:14 PM, Bhargavi Duvvuri wrote: > >> Hello James, >> >> The one I am using: >> >> [1]*primeviewhsrefseqcdf_1.36.**0* AnnotationDbi_1.20.3 >> >> [3] Biobase_2.18.0 BiocGenerics_0.4.0 >> >> >> Your primeview package >> *primeviewhsrefseqcdf_16.0.0* >> * >> * >> My windows version: >> *PrimeViewHsREFSEQcdf_1.36.0 * >> * >> * >> As you ca see windows and Linux versions I am using are the same, except >> for uppercase and lowercase. On windows I get 34901 and on Linux i get >> 26308*. *If it was for the primeview package version, why would this work >> on windows? >> >> Please advise. >> > > I have been trying to advise, but you seem intent on not being advised. So > this is my last shot. Expect no more responses from me on this subject. > TYPE EXACTLY WHAT I HAVE WRITTEN BELOW AT AN R PROMPT ON YOUR LINUX BOX. > > library(BiocInstaller) > biocLite("**primeviewhsrefseqcdf") > > > >> Thank you >> * >> * >> *Bhargavi* >> >> >> >> On Tue, Dec 11, 2012 at 3:58 PM, James W. MacDonald <jmacdon@uw.edu<mailto:>> jmacdon@uw.edu>> wrote: >> >> >> >> On 12/11/2012 3:53 PM, Bhargavi Duvvuri wrote: >> >> Hello James, >> >> I am very new to R. >> >> I see minor change in the R version. >> >> My version of R sessionInfo() >> >> *R version 2.15.0 (2012-03-30)* >> >> Platform: x86_64-unknown-linux-gnu (64-bit) >> loaded via a namespace (and not attached): >> [1] DBI_0.2-5 IRanges_1.16.4 parallel_2.15.0 RSQLite_0.11.2 >> [5] stats4_2.15.0 tools_2.15.0 >> >> Your version of sessionInfo(): >> >> *R version 2.15.1 (2012-06-22)* >> >> Platform: x86_64-unknown-linux-gnu (64-bit) >> other attached packages: >> >> loaded via a namespace (and not attached): >> [1] DBI_0.2-5 IRanges_1.16.4 parallel_2.15.1 RSQLite_0.11.2 >> [5] stats4_2.15.1 tools_2.15.1 >> >> Do you think this minor difference would make effect? >> >> >> No. But if you re-read what I have said below, you will note I am >> not talking about the version of R you are using. Instead, I am >> talking about the version of primeviewhsrefseqcdf you are using. >> >> The package you are using is different from the one I am using, >> and since you didn't load it before running sessionInfo() I have >> no idea what you are using. If the version is the same as mine, >> then I would assume there was a problem somewhere along the line >> and you need to re-install. Well, actually I think you need to >> re-install regardless. >> >> So try that and see if the updated version of that package looks OK. >> >> Best, >> >> Jim >> >> >> Thank you >> >> Bhargavi >> >> >> >> On Tue, Dec 11, 2012 at 3:18 PM, James W. MacDonald >> <jmacdon@uw.edu <mailto:jmacdon@uw.edu=""> <mailto:jmacdon@uw.edu>> >> <mailto:jmacdon@uw.edu>>> wrote: >> >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> >> >> >> -- Bhargavi Duvvuri M.Sc, Ph.D >> TAS/CAN Postdoctoral Research Fellow >> The Hospital for Sick Children Research Institute >> Division of Cell Biology >> MARS Centre - Toronto Medical Discovery Tower >> 101 College street, Rm 12-401 Bay C >> Toronto, ON, Canada M5G 1L7 >> Phone: 416-813-7780 <tel:416-813-7780> >> Fax: 416-813-8883 <tel:416-813-8883> >> email: bhargavi.duvvuri@sickkids.ca >> <mailto:bhargavi.duvvuri@**sickkids.ca<bhargavi.duvvuri@sickkids.ca> >> > >> <mailto:bhargavi.duvvuri@**sickkids.ca<bhargavi.duvvuri@sickkids.ca> >> >> <mailto:bhargavi.duvvuri@**sickkids.ca<bhargavi.duvvuri@sickkids.ca> >> >> >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> >> >> >> -- >> Bhargavi Duvvuri M.Sc, Ph.D >> TAS/CAN Postdoctoral Research Fellow >> The Hospital for Sick Children Research Institute >> Division of Cell Biology >> MARS Centre - Toronto Medical Discovery Tower >> 101 College street, Rm 12-401 Bay C >> Toronto, ON, Canada M5G 1L7 >> Phone: 416-813-7780 >> Fax: 416-813-8883 >> email: bhargavi.duvvuri@sickkids.ca <mailto:bhargavi.duvvuri@**>> sickkids.ca <bhargavi.duvvuri@sickkids.ca>> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- Bhargavi Duvvuri M.Sc, Ph.D TAS/CAN Postdoctoral Research Fellow The Hospital for Sick Children Research Institute Division of Cell Biology MARS Centre - Toronto Medical Discovery Tower 101 College street, Rm 12-401 Bay C Toronto, ON, Canada M5G 1L7 Phone: 416-813-7780 Fax: 416-813-8883 email: bhargavi.duvvuri@sickkids.ca [[alternative HTML version deleted]]
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Hello James, I am able to solve the issue by installing updated version of primeview and there were some minor unnoticed issues with R too. Thank you again for your help. Bhargavi On Tue, Dec 11, 2012 at 4:25 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Bhargavi, > > > On 12/11/2012 4:14 PM, Bhargavi Duvvuri wrote: > >> Hello James, >> >> The one I am using: >> >> [1]*primeviewhsrefseqcdf_1.36.**0* AnnotationDbi_1.20.3 >> >> [3] Biobase_2.18.0 BiocGenerics_0.4.0 >> >> >> Your primeview package >> *primeviewhsrefseqcdf_16.0.0* >> * >> * >> My windows version: >> *PrimeViewHsREFSEQcdf_1.36.0 * >> * >> * >> As you ca see windows and Linux versions I am using are the same, except >> for uppercase and lowercase. On windows I get 34901 and on Linux i get >> 26308*. *If it was for the primeview package version, why would this work >> on windows? >> >> Please advise. >> > > I have been trying to advise, but you seem intent on not being advised. So > this is my last shot. Expect no more responses from me on this subject. > TYPE EXACTLY WHAT I HAVE WRITTEN BELOW AT AN R PROMPT ON YOUR LINUX BOX. > > library(BiocInstaller) > biocLite("**primeviewhsrefseqcdf") > > > >> Thank you >> * >> * >> *Bhargavi* >> >> >> >> On Tue, Dec 11, 2012 at 3:58 PM, James W. MacDonald <jmacdon@uw.edu<mailto:>> jmacdon@uw.edu>> wrote: >> >> >> >> On 12/11/2012 3:53 PM, Bhargavi Duvvuri wrote: >> >> Hello James, >> >> I am very new to R. >> >> I see minor change in the R version. >> >> My version of R sessionInfo() >> >> *R version 2.15.0 (2012-03-30)* >> >> Platform: x86_64-unknown-linux-gnu (64-bit) >> loaded via a namespace (and not attached): >> [1] DBI_0.2-5 IRanges_1.16.4 parallel_2.15.0 RSQLite_0.11.2 >> [5] stats4_2.15.0 tools_2.15.0 >> >> Your version of sessionInfo(): >> >> *R version 2.15.1 (2012-06-22)* >> >> Platform: x86_64-unknown-linux-gnu (64-bit) >> other attached packages: >> >> loaded via a namespace (and not attached): >> [1] DBI_0.2-5 IRanges_1.16.4 parallel_2.15.1 RSQLite_0.11.2 >> [5] stats4_2.15.1 tools_2.15.1 >> >> Do you think this minor difference would make effect? >> >> >> No. But if you re-read what I have said below, you will note I am >> not talking about the version of R you are using. Instead, I am >> talking about the version of primeviewhsrefseqcdf you are using. >> >> The package you are using is different from the one I am using, >> and since you didn't load it before running sessionInfo() I have >> no idea what you are using. If the version is the same as mine, >> then I would assume there was a problem somewhere along the line >> and you need to re-install. Well, actually I think you need to >> re-install regardless. >> >> So try that and see if the updated version of that package looks OK. >> >> Best, >> >> Jim >> >> >> Thank you >> >> Bhargavi >> >> >> >> On Tue, Dec 11, 2012 at 3:18 PM, James W. MacDonald >> <jmacdon@uw.edu <mailto:jmacdon@uw.edu=""> <mailto:jmacdon@uw.edu>> >> <mailto:jmacdon@uw.edu>>> wrote: >> >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> >> >> >> -- Bhargavi Duvvuri M.Sc, Ph.D >> TAS/CAN Postdoctoral Research Fellow >> The Hospital for Sick Children Research Institute >> Division of Cell Biology >> MARS Centre - Toronto Medical Discovery Tower >> 101 College street, Rm 12-401 Bay C >> Toronto, ON, Canada M5G 1L7 >> Phone: 416-813-7780 <tel:416-813-7780> >> Fax: 416-813-8883 <tel:416-813-8883> >> email: bhargavi.duvvuri@sickkids.ca >> <mailto:bhargavi.duvvuri@**sickkids.ca<bhargavi.duvvuri@sickkids.ca> >> > >> <mailto:bhargavi.duvvuri@**sickkids.ca<bhargavi.duvvuri@sickkids.ca> >> >> <mailto:bhargavi.duvvuri@**sickkids.ca<bhargavi.duvvuri@sickkids.ca> >> >> >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> >> >> >> -- >> Bhargavi Duvvuri M.Sc, Ph.D >> TAS/CAN Postdoctoral Research Fellow >> The Hospital for Sick Children Research Institute >> Division of Cell Biology >> MARS Centre - Toronto Medical Discovery Tower >> 101 College street, Rm 12-401 Bay C >> Toronto, ON, Canada M5G 1L7 >> Phone: 416-813-7780 >> Fax: 416-813-8883 >> email: bhargavi.duvvuri@sickkids.ca <mailto:bhargavi.duvvuri@**>> sickkids.ca <bhargavi.duvvuri@sickkids.ca>> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- Bhargavi Duvvuri M.Sc, Ph.D TAS/CAN Postdoctoral Research Fellow The Hospital for Sick Children Research Institute Division of Cell Biology MARS Centre - Toronto Medical Discovery Tower 101 College street, Rm 12-401 Bay C Toronto, ON, Canada M5G 1L7 Phone: 416-813-7780 Fax: 416-813-8883 email: bhargavi.duvvuri@sickkids.ca [[alternative HTML version deleted]]
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