affy( ) error with mas5()
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Ying Chen ▴ 110
@ying-chen-4756
Last seen 10.2 years ago
Hi guys, I use affy to process over 3800 affy U133Plus2 arrays. rma() went well, but mas5() gave me the error during background correcting: Error in matrix(.C("affy_background_adjust_R", as.double(as.vector(allintensities)), : long vectors (argument 1) are not supported in .Fortran I have been using affy() for a long time and this is the first time I run into such error. Any suggestion? Thanks a lot for the help! Ying > data <- ReadAffy() > eset <- mas5(data) background correction: mas PM/MM correction : mas expression values: mas background correcting... Error in matrix(.C("affy_background_adjust_R", as.double(as.vector(allintensities)), : long vectors (argument 1) are not supported in .Fortran > str(eset) Error in str(eset) : object 'eset' not found > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US [4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] hgu133plus2cdf_2.13.0 AnnotationDbi_1.24.0 affy_1.40.0 [4] Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affyio_1.30.0 BiocInstaller_1.12.0 DBI_0.2-7 [4] IRanges_1.20.7 preprocessCore_1.24.0 RSQLite_0.11.4 [7] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0 > -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Abugri James Sent: Wednesday, April 09, 2014 4:35 AM To: bioconductor at r-project.org Subject: [BioC] rehh package for iHS and Rsb Dear Bioconductor community, I have expressly read the manual and done the tutorial for the rehh package a dozen times, but still unable to apply it to my P. falciparum SNP data set. I have the SNP.INFO for P. falciparum. AND r scripts to call the genotypes and haplotypes. Has anybody got an experience in implementing this package. -- *ABUGRI, James* *Lecturer* *Department of Applied Chemistry and Biochemistry* *Faculty of Applied Sciences* *University For Development Studies, Navrongo Campus* *Mobile; +233244994359 or +233204088294* -- * "The information contained in this email and any attachments may be legally privileged and confidential. If you are not an intended recipient, you are hereby notified that any dissemination, distribution, or copying of this e-mail is strictly prohibited. If you have received this e-mail in error, please notify the sender and permanently delete the e-mail and any attachments immediately. You should not retain, copy or use this e-mail or any attachments for any purpose, nor disclose all or any part of the contents to any other person."* [[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 Confidentiality Note:\ This e-mail, and any attachment t...{{dropped:11}}
SNP affy PROcess SNP affy PROcess • 1.6k views
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@james-w-macdonald-5106
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Hi Ying, On 4/9/2014 10:21 AM, Ying Chen wrote: > Hi guys, > > I use affy to process over 3800 affy U133Plus2 arrays. rma() went well, but mas5() gave me the error during background correcting: > > Error in matrix(.C("affy_background_adjust_R", as.double(as.vector(allintensities)), : > long vectors (argument 1) are not supported in .Fortran > > I have been using affy() for a long time and this is the first time I run into such error. Any suggestion? In R-3.0.0 support for long vectors was implemented. The NEWS file for that release says * Many calls to |.C()| have been replaced by |.Call()| to allow long vectors to be supported (now or in the future). Regrettably several packages had copied the non-API |.C()| calls and so failed. * |.C()| and |.Fortran()| do not accept long vector inputs. This is a precaution as it is very unlikely that existing code will have been written to handle long vectors (and the *R* wrappers often assume that |length(x)| is an integer). So it appears we need to convert the .C() call in bg.correct.mas to a .Call() to accommodate these changes. I sort of doubt this will happen before the impending release, unfortunately. Best, Jim > > Thanks a lot for the help! > > Ying > >> data <- ReadAffy() >> eset <- mas5(data) > background correction: mas > PM/MM correction : mas > expression values: mas > background correcting... > Error in matrix(.C("affy_background_adjust_R", as.double(as.vector(allintensities)), : > long vectors (argument 1) are not supported in .Fortran >> str(eset) > Error in str(eset) : object 'eset' not found >> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US > [4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US > [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] hgu133plus2cdf_2.13.0 AnnotationDbi_1.24.0 affy_1.40.0 > [4] Biobase_2.22.0 BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.30.0 BiocInstaller_1.12.0 DBI_0.2-7 > [4] IRanges_1.20.7 preprocessCore_1.24.0 RSQLite_0.11.4 > [7] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0 > -----Original Message----- > From: bioconductor-bounces at r-project.org [mailto:bioconductor- bounces at r-project.org] On Behalf Of Abugri James > Sent: Wednesday, April 09, 2014 4:35 AM > To: bioconductor at r-project.org > Subject: [BioC] rehh package for iHS and Rsb > > Dear Bioconductor community, > I have expressly read the manual and done the tutorial for the rehh package a dozen times, but still unable to apply it to my P. falciparum SNP data set. I have the SNP.INFO for P. falciparum. AND r scripts to call the genotypes and haplotypes. Has anybody got an experience in implementing this package. > > -- > *ABUGRI, James* > *Lecturer* > *Department of Applied Chemistry and Biochemistry* *Faculty of Applied Sciences* *University For Development Studies, Navrongo Campus* *Mobile; +233244994359 or +233204088294* > > -- > * "The information contained in this email and any attachments may be legally privileged and confidential. If you are not an intended recipient, you are hereby notified that any dissemination, distribution, or copying of this e-mail is strictly prohibited. If you have received this e-mail in error, please notify the sender and permanently delete the e-mail and any attachments immediately. You should not retain, copy or use this e-mail or any attachments for any purpose, nor disclose all or any part of the contents to any other person."* > > [[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 > Confidentiality Note:\ This e-mail, and any attachment t...{{dropped:11}} > > _______________________________________________ > 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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On 04/09/2014 07:44 AM, James W. MacDonald wrote: > Hi Ying, > > > On 4/9/2014 10:21 AM, Ying Chen wrote: >> Hi guys, >> >> I use affy to process over 3800 affy U133Plus2 arrays. rma() went well, but >> mas5() gave me the error during background correcting: >> >> Error in matrix(.C("affy_background_adjust_R", >> as.double(as.vector(allintensities)), : >> long vectors (argument 1) are not supported in .Fortran >> >> I have been using affy() for a long time and this is the first time I run into >> such error. Any suggestion? > > In R-3.0.0 support for long vectors was implemented. The NEWS file for that > release says > > * > > Many calls to |.C()| have been replaced by |.Call()| to allow long > vectors to be supported (now or in the future). Regrettably several > packages had copied the non-API |.C()| calls and so failed. > > * > > |.C()| and |.Fortran()| do not accept long vector inputs. This is a > precaution as it is very unlikely that existing code will have been > written to handle long vectors (and the *R* wrappers often assume > that |length(x)| is an integer). > > > So it appears we need to convert the .C() call in bg.correct.mas to a .Call() to > accommodate these changes. I sort of doubt this will happen before the impending > release, unfortunately. To me this implies that length(allintensities) is greater than 2^31-1, or that it has gone through some intermediate stage that was larger than this. But that doesn't seem correct? If there's an easy way to reproduce this error then I'm happy to investigate... Martin > > Best, > > Jim > > >> >> Thanks a lot for the help! >> >> Ying >> >>> data <- ReadAffy() >>> eset <- mas5(data) >> background correction: mas >> PM/MM correction : mas >> expression values: mas >> background correcting... >> Error in matrix(.C("affy_background_adjust_R", >> as.double(as.vector(allintensities)), : >> long vectors (argument 1) are not supported in .Fortran >>> str(eset) >> Error in str(eset) : object 'eset' not found >>> sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US >> [4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US >> [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C >> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] hgu133plus2cdf_2.13.0 AnnotationDbi_1.24.0 affy_1.40.0 >> [4] Biobase_2.22.0 BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.30.0 BiocInstaller_1.12.0 DBI_0.2-7 >> [4] IRanges_1.20.7 preprocessCore_1.24.0 RSQLite_0.11.4 >> [7] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0 >> -----Original Message----- >> From: bioconductor-bounces at r-project.org >> [mailto:bioconductor-bounces at r-project.org] On Behalf Of Abugri James >> Sent: Wednesday, April 09, 2014 4:35 AM >> To: bioconductor at r-project.org >> Subject: [BioC] rehh package for iHS and Rsb >> >> Dear Bioconductor community, >> I have expressly read the manual and done the tutorial for the rehh package a >> dozen times, but still unable to apply it to my P. falciparum SNP data set. I >> have the SNP.INFO for P. falciparum. AND r scripts to call the genotypes and >> haplotypes. Has anybody got an experience in implementing this package. >> >> -- >> *ABUGRI, James* >> *Lecturer* >> *Department of Applied Chemistry and Biochemistry* *Faculty of Applied >> Sciences* *University For Development Studies, Navrongo Campus* *Mobile; >> +233244994359 or +233204088294* >> >> -- >> * "The information contained in this email and any attachments may be legally >> privileged and confidential. If you are not an intended recipient, you are >> hereby notified that any dissemination, distribution, or copying of this >> e-mail is strictly prohibited. If you have received this e-mail in error, >> please notify the sender and permanently delete the e-mail and any attachments >> immediately. You should not retain, copy or use this e-mail or any attachments >> for any purpose, nor disclose all or any part of the contents to any other >> person."* >> >> [[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 >> Confidentiality Note:\ This e-mail, and any attachment t...{{dropped:11}} >> >> _______________________________________________ >> 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 > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Hi Martin, > length(unlist(as.list(hgu133plus2cdf)))*3800 [1] 4592360800 > 2^31 [1] 2147483648 So allintensities is definitely longer than 2^31-1 Best, Jim On Wednesday, April 09, 2014 10:51:43 AM, Martin Morgan wrote: > On 04/09/2014 07:44 AM, James W. MacDonald wrote: >> Hi Ying, >> >> >> On 4/9/2014 10:21 AM, Ying Chen wrote: >>> Hi guys, >>> >>> I use affy to process over 3800 affy U133Plus2 arrays. rma() went >>> well, but >>> mas5() gave me the error during background correcting: >>> >>> Error in matrix(.C("affy_background_adjust_R", >>> as.double(as.vector(allintensities)), : >>> long vectors (argument 1) are not supported in .Fortran >>> >>> I have been using affy() for a long time and this is the first time >>> I run into >>> such error. Any suggestion? >> >> In R-3.0.0 support for long vectors was implemented. The NEWS file >> for that >> release says >> >> * >> >> Many calls to |.C()| have been replaced by |.Call()| to allow long >> vectors to be supported (now or in the future). Regrettably several >> packages had copied the non-API |.C()| calls and so failed. >> >> * >> >> |.C()| and |.Fortran()| do not accept long vector inputs. This is a >> precaution as it is very unlikely that existing code will have been >> written to handle long vectors (and the *R* wrappers often assume >> that |length(x)| is an integer). >> >> >> So it appears we need to convert the .C() call in bg.correct.mas to a >> .Call() to >> accommodate these changes. I sort of doubt this will happen before >> the impending >> release, unfortunately. > > To me this implies that length(allintensities) is greater than 2^31-1, > or that it has gone through some intermediate stage that was larger > than this. But that doesn't seem correct? > > If there's an easy way to reproduce this error then I'm happy to > investigate... > > Martin > >> >> Best, >> >> Jim >> >> >>> >>> Thanks a lot for the help! >>> >>> Ying >>> >>>> data <- ReadAffy() >>>> eset <- mas5(data) >>> background correction: mas >>> PM/MM correction : mas >>> expression values: mas >>> background correcting... >>> Error in matrix(.C("affy_background_adjust_R", >>> as.double(as.vector(allintensities)), : >>> long vectors (argument 1) are not supported in .Fortran >>>> str(eset) >>> Error in str(eset) : object 'eset' not found >>>> sessionInfo() >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US >>> [4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US >>> [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C >>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] hgu133plus2cdf_2.13.0 AnnotationDbi_1.24.0 affy_1.40.0 >>> [4] Biobase_2.22.0 BiocGenerics_0.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.30.0 BiocInstaller_1.12.0 DBI_0.2-7 >>> [4] IRanges_1.20.7 preprocessCore_1.24.0 RSQLite_0.11.4 >>> [7] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0 >>> -----Original Message----- >>> From: bioconductor-bounces at r-project.org >>> [mailto:bioconductor-bounces at r-project.org] On Behalf Of Abugri James >>> Sent: Wednesday, April 09, 2014 4:35 AM >>> To: bioconductor at r-project.org >>> Subject: [BioC] rehh package for iHS and Rsb >>> >>> Dear Bioconductor community, >>> I have expressly read the manual and done the tutorial for the rehh >>> package a >>> dozen times, but still unable to apply it to my P. falciparum SNP >>> data set. I >>> have the SNP.INFO for P. falciparum. AND r scripts to call the >>> genotypes and >>> haplotypes. Has anybody got an experience in implementing this package. >>> >>> -- >>> *ABUGRI, James* >>> *Lecturer* >>> *Department of Applied Chemistry and Biochemistry* *Faculty of Applied >>> Sciences* *University For Development Studies, Navrongo Campus* >>> *Mobile; >>> +233244994359 or +233204088294* >>> >>> -- >>> * "The information contained in this email and any attachments may >>> be legally >>> privileged and confidential. If you are not an intended recipient, >>> you are >>> hereby notified that any dissemination, distribution, or copying of >>> this >>> e-mail is strictly prohibited. If you have received this e-mail in >>> error, >>> please notify the sender and permanently delete the e-mail and any >>> attachments >>> immediately. You should not retain, copy or use this e-mail or any >>> attachments >>> for any purpose, nor disclose all or any part of the contents to any >>> other >>> person."* >>> >>> [[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 >>> Confidentiality Note:\ This e-mail, and any attachment >>> t...{{dropped:11}} >>> >>> _______________________________________________ >>> 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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Hi guys, Thanks a lot for the help and sorry for getting back to you so late :(. Now I got confused. Does it mean affy() cannot do a MAS5 of 3869 HG- U133_Plus_2 arrays with affy CDF because of the setting of R long vectors, or I did something wrong? I did a RMA with no problem. Thanks, Ying > Date: Wed, 9 Apr 2014 10:58:44 -0400 > From: jmacdon@uw.edu > To: mtmorgan@fhcrc.org > CC: bioconductor@r-project.org > Subject: Re: [BioC] affy( ) error with mas5() > > Hi Martin, > > > length(unlist(as.list(hgu133plus2cdf)))*3800 > [1] 4592360800 > > 2^31 > [1] 2147483648 > > So allintensities is definitely longer than 2^31-1 > > Best, > > Jim > > > > On Wednesday, April 09, 2014 10:51:43 AM, Martin Morgan wrote: > > On 04/09/2014 07:44 AM, James W. MacDonald wrote: > >> Hi Ying, > >> > >> > >> On 4/9/2014 10:21 AM, Ying Chen wrote: > >>> Hi guys, > >>> > >>> I use affy to process over 3800 affy U133Plus2 arrays. rma() went > >>> well, but > >>> mas5() gave me the error during background correcting: > >>> > >>> Error in matrix(.C("affy_background_adjust_R", > >>> as.double(as.vector(allintensities)), : > >>> long vectors (argument 1) are not supported in .Fortran > >>> > >>> I have been using affy() for a long time and this is the first time > >>> I run into > >>> such error. Any suggestion? > >> > >> In R-3.0.0 support for long vectors was implemented. The NEWS file > >> for that > >> release says > >> > >> * > >> > >> Many calls to |.C()| have been replaced by |.Call()| to allow long > >> vectors to be supported (now or in the future). Regrettably several > >> packages had copied the non-API |.C()| calls and so failed. > >> > >> * > >> > >> |.C()| and |.Fortran()| do not accept long vector inputs. This is a > >> precaution as it is very unlikely that existing code will have been > >> written to handle long vectors (and the *R* wrappers often assume > >> that |length(x)| is an integer). > >> > >> > >> So it appears we need to convert the .C() call in bg.correct.mas to a > >> .Call() to > >> accommodate these changes. I sort of doubt this will happen before > >> the impending > >> release, unfortunately. > > > > To me this implies that length(allintensities) is greater than 2^31-1, > > or that it has gone through some intermediate stage that was larger > > than this. But that doesn't seem correct? > > > > If there's an easy way to reproduce this error then I'm happy to > > investigate... > > > > Martin > > > >> > >> Best, > >> > >> Jim > >> > >> > >>> > >>> Thanks a lot for the help! > >>> > >>> Ying > >>> > >>>> data <- ReadAffy() > >>>> eset <- mas5(data) > >>> background correction: mas > >>> PM/MM correction : mas > >>> expression values: mas > >>> background correcting... > >>> Error in matrix(.C("affy_background_adjust_R", > >>> as.double(as.vector(allintensities)), : > >>> long vectors (argument 1) are not supported in .Fortran > >>>> str(eset) > >>> Error in str(eset) : object 'eset' not found > >>>> sessionInfo() > >>> R version 3.0.2 (2013-09-25) > >>> Platform: x86_64-unknown-linux-gnu (64-bit) > >>> > >>> locale: > >>> [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US > >>> [4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US > >>> [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C > >>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C > >>> > >>> attached base packages: > >>> [1] parallel stats graphics grDevices utils datasets methods > >>> [8] base > >>> > >>> other attached packages: > >>> [1] hgu133plus2cdf_2.13.0 AnnotationDbi_1.24.0 affy_1.40.0 > >>> [4] Biobase_2.22.0 BiocGenerics_0.8.0 > >>> > >>> loaded via a namespace (and not attached): > >>> [1] affyio_1.30.0 BiocInstaller_1.12.0 DBI_0.2-7 > >>> [4] IRanges_1.20.7 preprocessCore_1.24.0 RSQLite_0.11.4 > >>> [7] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0 > >>> -----Original Message----- > >>> From: bioconductor-bounces@r-project.org > >>> [mailto:bioconductor-bounces@r-project.org] On Behalf Of Abugri James > >>> Sent: Wednesday, April 09, 2014 4:35 AM > >>> To: bioconductor@r-project.org > >>> Subject: [BioC] rehh package for iHS and Rsb > >>> > >>> Dear Bioconductor community, > >>> I have expressly read the manual and done the tutorial for the rehh > >>> package a > >>> dozen times, but still unable to apply it to my P. falciparum SNP > >>> data set. I > >>> have the SNP.INFO for P. falciparum. AND r scripts to call the > >>> genotypes and > >>> haplotypes. Has anybody got an experience in implementing this package. > >>> > >>> -- > >>> *ABUGRI, James* > >>> *Lecturer* > >>> *Department of Applied Chemistry and Biochemistry* *Faculty of Applied > >>> Sciences* *University For Development Studies, Navrongo Campus* > >>> *Mobile; > >>> +233244994359 or +233204088294* > >>> > >>> -- > >>> * "The information contained in this email and any attachments may > >>> be legally > >>> privileged and confidential. If you are not an intended recipient, > >>> you are > >>> hereby notified that any dissemination, distribution, or copying of > >>> this > >>> e-mail is strictly prohibited. If you have received this e-mail in > >>> error, > >>> please notify the sender and permanently delete the e-mail and any > >>> attachments > >>> immediately. You should not retain, copy or use this e-mail or any > >>> attachments > >>> for any purpose, nor disclose all or any part of the contents to any > >>> other > >>> person."* > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor@r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: > >>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> Confidentiality Note:\ This e-mail, and any attachment > >>> t...{{dropped:11}} > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor@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@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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Hi Ying, Yes, it has to do with long vectors in R. For RMA you don't generate a long vector, but instead pass in a matrix to the C code (which will be converted to a vector, but R doesn't know about that as far as I can tell). If you really care about using mas5(), you could install R-2.15.1 and its version of bioconductor and run mas5. The code for that function hasn't changed for years now (like since 2005), so it will do the same thing with R-2.15.1 that it would do with R-3.1.0. Best, Jim On 4/25/2014 9:31 AM, ying chen wrote: > Hi guys, > > Thanks a lot for the help and sorry for getting back to you so late :(. > > Now I got confused. Does it mean affy() cannot do a MAS5 of 3869 > HG-U133_Plus_2 arrays with affy CDF because of the setting of R long > vectors, or I did something wrong? I did a RMA with no problem. > > Thanks, > > Ying > > > Date: Wed, 9 Apr 2014 10:58:44 -0400 > > From: jmacdon at uw.edu > > To: mtmorgan at fhcrc.org > > CC: bioconductor at r-project.org > > Subject: Re: [BioC] affy( ) error with mas5() > > > > Hi Martin, > > > > > length(unlist(as.list(hgu133plus2cdf)))*3800 > > [1] 4592360800 > > > 2^31 > > [1] 2147483648 > > > > So allintensities is definitely longer than 2^31-1 > > > > Best, > > > > Jim > > > > > > > > On Wednesday, April 09, 2014 10:51:43 AM, Martin Morgan wrote: > > > On 04/09/2014 07:44 AM, James W. MacDonald wrote: > > >> Hi Ying, > > >> > > >> > > >> On 4/9/2014 10:21 AM, Ying Chen wrote: > > >>> Hi guys, > > >>> > > >>> I use affy to process over 3800 affy U133Plus2 arrays. rma() went > > >>> well, but > > >>> mas5() gave me the error during background correcting: > > >>> > > >>> Error in matrix(.C("affy_background_adjust_R", > > >>> as.double(as.vector(allintensities)), : > > >>> long vectors (argument 1) are not supported in .Fortran > > >>> > > >>> I have been using affy() for a long time and this is the first time > > >>> I run into > > >>> such error. Any suggestion? > > >> > > >> In R-3.0.0 support for long vectors was implemented. The NEWS file > > >> for that > > >> release says > > >> > > >> * > > >> > > >> Many calls to |.C()| have been replaced by |.Call()| to allow long > > >> vectors to be supported (now or in the future). Regrettably several > > >> packages had copied the non-API |.C()| calls and so failed. > > >> > > >> * > > >> > > >> |.C()| and |.Fortran()| do not accept long vector inputs. This is a > > >> precaution as it is very unlikely that existing code will have been > > >> written to handle long vectors (and the *R* wrappers often assume > > >> that |length(x)| is an integer). > > >> > > >> > > >> So it appears we need to convert the .C() call in bg.correct.mas to a > > >> .Call() to > > >> accommodate these changes. I sort of doubt this will happen before > > >> the impending > > >> release, unfortunately. > > > > > > To me this implies that length(allintensities) is greater than 2^31-1, > > > or that it has gone through some intermediate stage that was larger > > > than this. But that doesn't seem correct? > > > > > > If there's an easy way to reproduce this error then I'm happy to > > > investigate... > > > > > > Martin > > > > > >> > > >> Best, > > >> > > >> Jim > > >> > > >> > > >>> > > >>> Thanks a lot for the help! > > >>> > > >>> Ying > > >>> > > >>>> data <- ReadAffy() > > >>>> eset <- mas5(data) > > >>> background correction: mas > > >>> PM/MM correction : mas > > >>> expression values: mas > > >>> background correcting... > > >>> Error in matrix(.C("affy_background_adjust_R", > > >>> as.double(as.vector(allintensities)), : > > >>> long vectors (argument 1) are not supported in .Fortran > > >>>> str(eset) > > >>> Error in str(eset) : object 'eset' not found > > >>>> sessionInfo() > > >>> R version 3.0.2 (2013-09-25) > > >>> Platform: x86_64-unknown-linux-gnu (64-bit) > > >>> > > >>> locale: > > >>> [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US > > >>> [4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US > > >>> [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C > > >>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C > > >>> > > >>> attached base packages: > > >>> [1] parallel stats graphics grDevices utils datasets methods > > >>> [8] base > > >>> > > >>> other attached packages: > > >>> [1] hgu133plus2cdf_2.13.0 AnnotationDbi_1.24.0 affy_1.40.0 > > >>> [4] Biobase_2.22.0 BiocGenerics_0.8.0 > > >>> > > >>> loaded via a namespace (and not attached): > > >>> [1] affyio_1.30.0 BiocInstaller_1.12.0 DBI_0.2-7 > > >>> [4] IRanges_1.20.7 preprocessCore_1.24.0 RSQLite_0.11.4 > > >>> [7] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0 > > >>> -----Original Message----- > > >>> From: bioconductor-bounces at r-project.org > > >>> [mailto:bioconductor-bounces at r-project.org] On Behalf Of Abugri > James > > >>> Sent: Wednesday, April 09, 2014 4:35 AM > > >>> To: bioconductor at r-project.org > > >>> Subject: [BioC] rehh package for iHS and Rsb > > >>> > > >>> Dear Bioconductor community, > > >>> I have expressly read the manual and done the tutorial for the rehh > > >>> package a > > >>> dozen times, but still unable to apply it to my P. falciparum SNP > > >>> data set. I > > >>> have the SNP.INFO for P. falciparum. AND r scripts to call the > > >>> genotypes and > > >>> haplotypes. Has anybody got an experience in implementing this > package. > > >>> > > >>> -- > > >>> *ABUGRI, James* > > >>> *Lecturer* > > >>> *Department of Applied Chemistry and Biochemistry* *Faculty of > Applied > > >>> Sciences* *University For Development Studies, Navrongo Campus* > > >>> *Mobile; > > >>> +233244994359 or +233204088294* > > >>> > > >>> -- > > >>> * "The information contained in this email and any attachments may > > >>> be legally > > >>> privileged and confidential. If you are not an intended recipient, > > >>> you are > > >>> hereby notified that any dissemination, distribution, or copying of > > >>> this > > >>> e-mail is strictly prohibited. If you have received this e-mail in > > >>> error, > > >>> please notify the sender and permanently delete the e-mail and any > > >>> attachments > > >>> immediately. You should not retain, copy or use this e-mail or any > > >>> attachments > > >>> for any purpose, nor disclose all or any part of the contents to any > > >>> other > > >>> person."* > > >>> > > >>> [[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 > > >>> Confidentiality Note:\ This e-mail, and any attachment > > >>> t...{{dropped:11}} > > >>> > > >>> _______________________________________________ > > >>> 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 -- 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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