Problem with affy mas5 on Linux but not Windows...
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James Carman ▴ 150
@james-carman-4265
Last seen 9.7 years ago
If I try to run this code on Linux, it fails, but it works on Windows: > library(affy) > aff <- ReadAffy() > m5 <- mas5(aff) background correction: mas PM/MM correction : mas expression values: mas background correcting...Error in as.vector(data) : NAs in foreign function call (arg 2) Here's the result of sessionInfo(): > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133a2cdf_2.7.0 affy_1.28.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 preprocessCore_1.10.0 tools_2.12.1 Here's my platform: > uname -a Linux carman-op755 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23 16:04:50 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux Here's the version of R that I'm running: > rpm -qa | grep R- R-core-2.12.1-1.fc14.x86_64 R-devel-2.12.1-1.fc14.x86_64 R-2.12.1-1.fc14.x86_64 We have used this process in the past and it has worked fine. I got a new computer and installed the latest Bioconductor package(s) on it and now I'm getting this failure. Any ideas? Thank you, James Carman
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Hi James, On 1/28/2011 11:00 AM, James Carman wrote: > If I try to run this code on Linux, it fails, but it works on Windows: > >> library(affy) >> aff<- ReadAffy() >> m5<- mas5(aff) > background correction: mas > PM/MM correction : mas > expression values: mas > background correcting...Error in as.vector(data) : NAs in foreign > function call (arg 2) Let's start with something simple. Can you run mas5() on the Dilution data from the affydata package? I get > library(affydata) Loading required package: affy Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > data(Dilution) > m5 <- mas5(Dilution) background correction: mas PM/MM correction : mas expression values: mas background correcting...done. 12625 ids to be processed | | |####################| > sessionInfo() R version 2.12.0 beta (2010-09-30 r53083) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915 [7] LC_PAPER=en_US.iso885915 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu95av2cdf_2.7.0 affydata_1.11.10 affy_1.28.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.0 Best, Jim > > Here's the result of sessionInfo(): >> sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 > [7] LC_PAPER=en_US.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu133a2cdf_2.7.0 affy_1.28.0 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 preprocessCore_1.10.0 tools_2.12.1 > > Here's my platform: > >> uname -a > Linux carman-op755 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23 16:04:50 > UTC 2010 x86_64 x86_64 x86_64 GNU/Linux > > Here's the version of R that I'm running: > >> rpm -qa | grep R- > R-core-2.12.1-1.fc14.x86_64 > R-devel-2.12.1-1.fc14.x86_64 > R-2.12.1-1.fc14.x86_64 > > > We have used this process in the past and it has worked fine. I got a > new computer and installed the latest Bioconductor package(s) on it > and now I'm getting this failure. Any ideas? > > Thank you, > > James Carman > > _______________________________________________ > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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Looks like that worked for me (after it downloaded hgu95av2cdf of course). So, what does that mean? On Fri, Jan 28, 2011 at 11:40 AM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi James, > > On 1/28/2011 11:00 AM, James Carman wrote: >> >> If I try to run this code on Linux, it fails, but it works on Windows: >> >>> library(affy) >>> aff<- ReadAffy() >>> m5<- mas5(aff) >> >> background correction: mas >> PM/MM correction : mas >> expression values: mas >> background correcting...Error in as.vector(data) : NAs in foreign >> function call (arg 2) > > Let's start with something simple. Can you run mas5() on the Dilution data > from the affydata package? I get > >> library(affydata) > Loading required package: affy > Loading required package: Biobase > > Welcome to Bioconductor > > ?Vignettes contain introductory material. To view, type > ?'openVignette()'. To cite Bioconductor, see > ?'citation("Biobase")' and for packages 'citation(pkgname)'. > >> data(Dilution) >> m5 <- mas5(Dilution) > background correction: mas > PM/MM correction : mas > expression values: mas > background correcting...done. > 12625 ids to be processed > | ? ? ? ? ? ? ? ? ? ?| > |####################| >> sessionInfo() > R version 2.12.0 beta (2010-09-30 r53083) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > ?[1] LC_CTYPE=en_US.iso885915 ? ? ? LC_NUMERIC=C > ?[3] LC_TIME=en_US.iso885915 ? ? ? ?LC_COLLATE=en_US.iso885915 > ?[5] LC_MONETARY=C ? ? ? ? ? ? ? ? ?LC_MESSAGES=en_US.iso885915 > ?[7] LC_PAPER=en_US.iso885915 ? ? ? LC_NAME=C > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? ? ? LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] hgu95av2cdf_2.7.0 affydata_1.11.10 ?affy_1.28.0 ? ? ? Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 ? ? ? ? preprocessCore_1.12.0 tools_2.12.0 > > Best, > > Jim > > >> >> Here's the result of sessionInfo(): >>> >>> sessionInfo() >> >> R version 2.12.1 (2010-12-16) >> Platform: x86_64-redhat-linux-gnu (64-bit) >> >> locale: >> ?[1] LC_CTYPE=en_US.utf8 ? ? ? LC_NUMERIC=C >> ?[3] LC_TIME=en_US.utf8 ? ? ? ?LC_COLLATE=en_US.utf8 >> ?[5] LC_MONETARY=C ? ? ? ? ? ? LC_MESSAGES=en_US.utf8 >> ?[7] LC_PAPER=en_US.utf8 ? ? ? LC_NAME=C >> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ?LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] hgu133a2cdf_2.7.0 affy_1.28.0 ? ? ? Biobase_2.10.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.16.0 ? ? ? ? preprocessCore_1.10.0 tools_2.12.1 >> >> Here's my platform: >> >>> uname -a >> >> Linux carman-op755 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23 16:04:50 >> UTC 2010 x86_64 x86_64 x86_64 GNU/Linux >> >> Here's the version of R that I'm running: >> >>> rpm -qa | grep R- >> >> R-core-2.12.1-1.fc14.x86_64 >> R-devel-2.12.1-1.fc14.x86_64 >> R-2.12.1-1.fc14.x86_64 >> >> >> We have used this process in the past and it has worked fine. ?I got a >> new computer and installed the latest Bioconductor package(s) on it >> and now I'm getting this failure. ?Any ideas? >> >> Thank you, >> >> James Carman >> >> _______________________________________________ >> 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 > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues >
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On 1/28/2011 11:47 AM, James Carman wrote: > Looks like that worked for me (after it downloaded hgu95av2cdf of > course). So, what does that mean? It means there isn't any weird Linux/mas5() interaction going on, so we can look at your data. The error you report indicates you have some NA values in your data somewhere. So the first step is to check. anyis.na(exprs(aff))) This should return TRUE. If so, you can track it down to the 'bad' celfile by apply(exprs(aff), 2, function(x) anyis.na(x))) and then try re-uploading that celfile to your Linux box. If not, you can try debug(bg.correct.mas) bg.correct.mas(aff) and step through the function. The error comes at the line corrected <- matrix(.C("affy_background_adjust_R", as.double(as.vector(allintensities)), as.integer(allx), as.integer(ally), as.integer(nprobes), as.integer(nchips), as.integer(rows), as.integer(cols), as.integer(griddim), PACKAGE = "affy")[[1]], nprobes, nchips) where the data are passed off to a C function. Right before that step you can test the objects 'allx', 'ally' and 'nprobes' for any NA values. Note here that while in the debugger, R shows you the *next* line it is going to interpret, so when you see the above line you can test those objects for the presence of NA values. Let us know what you find! Best, Jim > > On Fri, Jan 28, 2011 at 11:40 AM, James W. MacDonald > <jmacdon at="" med.umich.edu=""> wrote: >> Hi James, >> >> On 1/28/2011 11:00 AM, James Carman wrote: >>> >>> If I try to run this code on Linux, it fails, but it works on Windows: >>> >>>> library(affy) >>>> aff<- ReadAffy() >>>> m5<- mas5(aff) >>> >>> background correction: mas >>> PM/MM correction : mas >>> expression values: mas >>> background correcting...Error in as.vector(data) : NAs in foreign >>> function call (arg 2) >> >> Let's start with something simple. Can you run mas5() on the Dilution data >> from the affydata package? I get >> >>> library(affydata) >> Loading required package: affy >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >>> data(Dilution) >>> m5<- mas5(Dilution) >> background correction: mas >> PM/MM correction : mas >> expression values: mas >> background correcting...done. >> 12625 ids to be processed >> | | >> |####################| >>> sessionInfo() >> R version 2.12.0 beta (2010-09-30 r53083) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C >> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915 >> [7] LC_PAPER=en_US.iso885915 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] hgu95av2cdf_2.7.0 affydata_1.11.10 affy_1.28.0 Biobase_2.10.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.0 >> >> Best, >> >> Jim >> >> >>> >>> Here's the result of sessionInfo(): >>>> >>>> sessionInfo() >>> >>> R version 2.12.1 (2010-12-16) >>> Platform: x86_64-redhat-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 >>> [7] LC_PAPER=en_US.utf8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] hgu133a2cdf_2.7.0 affy_1.28.0 Biobase_2.10.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.16.0 preprocessCore_1.10.0 tools_2.12.1 >>> >>> Here's my platform: >>> >>>> uname -a >>> >>> Linux carman-op755 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23 16:04:50 >>> UTC 2010 x86_64 x86_64 x86_64 GNU/Linux >>> >>> Here's the version of R that I'm running: >>> >>>> rpm -qa | grep R- >>> >>> R-core-2.12.1-1.fc14.x86_64 >>> R-devel-2.12.1-1.fc14.x86_64 >>> R-2.12.1-1.fc14.x86_64 >>> >>> >>> We have used this process in the past and it has worked fine. I got a >>> new computer and installed the latest Bioconductor package(s) on it >>> and now I'm getting this failure. Any ideas? >>> >>> Thank you, >>> >>> James Carman >>> >>> _______________________________________________ >>> 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 >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> > > _______________________________________________ > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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I tried what you recommended: > library(affy) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > aff = ReadAffy() > anyis.na(exprs(aff))) [1] FALSE > m5 = mas5(aff) background correction: mas PM/MM correction : mas expression values: mas background correcting...Error in as.vector(data) : NAs in foreign function call (arg 2) So, no NA values in my data. On Fri, Jan 28, 2011 at 12:41 PM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > > On 1/28/2011 11:47 AM, James Carman wrote: >> >> Looks like that worked for me (after it downloaded hgu95av2cdf of >> course). ?So, what does that mean? > > It means there isn't any weird Linux/mas5() interaction going on, so we can > look at your data. The error you report indicates you have some NA values in > your data somewhere. So the first step is to check. > > anyis.na(exprs(aff))) > > This should return TRUE. If so, you can track it down to the 'bad' celfile > by > > apply(exprs(aff), 2, function(x) anyis.na(x))) > > and then try re-uploading that celfile to your Linux box. > > If not, you can try > > debug(bg.correct.mas) > bg.correct.mas(aff) > > and step through the function. The error comes at the line > > ?corrected <- matrix(.C("affy_background_adjust_R", > as.double(as.vector(allintensities)), > ? ? ? ?as.integer(allx), as.integer(ally), as.integer(nprobes), > ? ? ? ?as.integer(nchips), as.integer(rows), as.integer(cols), > ? ? ? ?as.integer(griddim), PACKAGE = "affy")[[1]], nprobes, > ? ? ? ?nchips) > > where the data are passed off to a C function. Right before that step you > can test the objects 'allx', 'ally' and 'nprobes' for any NA values. Note > here that while in the debugger, R shows you the *next* line it is going to > interpret, so when you see the above line you can test those objects for the > presence of NA values. > > Let us know what you find! > > Best, > > Jim > > > > > >> >> On Fri, Jan 28, 2011 at 11:40 AM, James W. MacDonald >> <jmacdon at="" med.umich.edu=""> ?wrote: >>> >>> Hi James, >>> >>> On 1/28/2011 11:00 AM, James Carman wrote: >>>> >>>> If I try to run this code on Linux, it fails, but it works on Windows: >>>> >>>>> library(affy) >>>>> aff<- ReadAffy() >>>>> m5<- mas5(aff) >>>> >>>> background correction: mas >>>> PM/MM correction : mas >>>> expression values: mas >>>> background correcting...Error in as.vector(data) : NAs in foreign >>>> function call (arg 2) >>> >>> Let's start with something simple. Can you run mas5() on the Dilution >>> data >>> from the affydata package? I get >>> >>>> library(affydata) >>> >>> Loading required package: affy >>> Loading required package: Biobase >>> >>> Welcome to Bioconductor >>> >>> ?Vignettes contain introductory material. To view, type >>> ?'openVignette()'. To cite Bioconductor, see >>> ?'citation("Biobase")' and for packages 'citation(pkgname)'. >>> >>>> data(Dilution) >>>> m5<- mas5(Dilution) >>> >>> background correction: mas >>> PM/MM correction : mas >>> expression values: mas >>> background correcting...done. >>> 12625 ids to be processed >>> | ? ? ? ? ? ? ? ? ? ?| >>> |####################| >>>> >>>> sessionInfo() >>> >>> R version 2.12.0 beta (2010-09-30 r53083) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> ?[1] LC_CTYPE=en_US.iso885915 ? ? ? LC_NUMERIC=C >>> ?[3] LC_TIME=en_US.iso885915 ? ? ? ?LC_COLLATE=en_US.iso885915 >>> ?[5] LC_MONETARY=C ? ? ? ? ? ? ? ? ?LC_MESSAGES=en_US.iso885915 >>> ?[7] LC_PAPER=en_US.iso885915 ? ? ? LC_NAME=C >>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? ? ? LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>> >>> other attached packages: >>> [1] hgu95av2cdf_2.7.0 affydata_1.11.10 ?affy_1.28.0 ? ? ? Biobase_2.10.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.18.0 ? ? ? ? preprocessCore_1.12.0 tools_2.12.0 >>> >>> Best, >>> >>> Jim >>> >>> >>>> >>>> Here's the result of sessionInfo(): >>>>> >>>>> sessionInfo() >>>> >>>> R version 2.12.1 (2010-12-16) >>>> Platform: x86_64-redhat-linux-gnu (64-bit) >>>> >>>> locale: >>>> ?[1] LC_CTYPE=en_US.utf8 ? ? ? LC_NUMERIC=C >>>> ?[3] LC_TIME=en_US.utf8 ? ? ? ?LC_COLLATE=en_US.utf8 >>>> ?[5] LC_MONETARY=C ? ? ? ? ? ? LC_MESSAGES=en_US.utf8 >>>> ?[7] LC_PAPER=en_US.utf8 ? ? ? LC_NAME=C >>>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ?LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>> >>>> other attached packages: >>>> [1] hgu133a2cdf_2.7.0 affy_1.28.0 ? ? ? Biobase_2.10.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affyio_1.16.0 ? ? ? ? preprocessCore_1.10.0 tools_2.12.1 >>>> >>>> Here's my platform: >>>> >>>>> uname -a >>>> >>>> Linux carman-op755 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23 16:04:50 >>>> UTC 2010 x86_64 x86_64 x86_64 GNU/Linux >>>> >>>> Here's the version of R that I'm running: >>>> >>>>> rpm -qa | grep R- >>>> >>>> R-core-2.12.1-1.fc14.x86_64 >>>> R-devel-2.12.1-1.fc14.x86_64 >>>> R-2.12.1-1.fc14.x86_64 >>>> >>>> >>>> We have used this process in the past and it has worked fine. ?I got a >>>> new computer and installed the latest Bioconductor package(s) on it >>>> and now I'm getting this failure. ?Any ideas? >>>> >>>> Thank you, >>>> >>>> James Carman >>>> >>>> _______________________________________________ >>>> 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 >>> Douglas Lab >>> University of Michigan >>> Department of Human Genetics >>> 5912 Buhl >>> 1241 E. Catherine St. >>> Ann Arbor MI 48109-5618 >>> 734-615-7826 >>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and should not >>> be >>> used for urgent or sensitive issues >>> >> >> _______________________________________________ >> 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 > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues >
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What do you get from traceback()? On 1/28/2011 12:47 PM, James Carman wrote: > I tried what you recommended: > >> library(affy) > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > >> aff = ReadAffy() >> anyis.na(exprs(aff))) > [1] FALSE >> m5 = mas5(aff) > background correction: mas > PM/MM correction : mas > expression values: mas > background correcting...Error in as.vector(data) : NAs in foreign > function call (arg 2) > > So, no NA values in my data. > > On Fri, Jan 28, 2011 at 12:41 PM, James W. MacDonald > <jmacdon at="" med.umich.edu=""> wrote: >> >> On 1/28/2011 11:47 AM, James Carman wrote: >>> >>> Looks like that worked for me (after it downloaded hgu95av2cdf of >>> course). So, what does that mean? >> >> It means there isn't any weird Linux/mas5() interaction going on, so we can >> look at your data. The error you report indicates you have some NA values in >> your data somewhere. So the first step is to check. >> >> anyis.na(exprs(aff))) >> >> This should return TRUE. If so, you can track it down to the 'bad' celfile >> by >> >> apply(exprs(aff), 2, function(x) anyis.na(x))) >> >> and then try re-uploading that celfile to your Linux box. >> >> If not, you can try >> >> debug(bg.correct.mas) >> bg.correct.mas(aff) >> >> and step through the function. The error comes at the line >> >> corrected<- matrix(.C("affy_background_adjust_R", >> as.double(as.vector(allintensities)), >> as.integer(allx), as.integer(ally), as.integer(nprobes), >> as.integer(nchips), as.integer(rows), as.integer(cols), >> as.integer(griddim), PACKAGE = "affy")[[1]], nprobes, >> nchips) >> >> where the data are passed off to a C function. Right before that step you >> can test the objects 'allx', 'ally' and 'nprobes' for any NA values. Note >> here that while in the debugger, R shows you the *next* line it is going to >> interpret, so when you see the above line you can test those objects for the >> presence of NA values. >> >> Let us know what you find! >> >> Best, >> >> Jim >> >> >> >> >> >>> >>> On Fri, Jan 28, 2011 at 11:40 AM, James W. MacDonald >>> <jmacdon at="" med.umich.edu=""> wrote: >>>> >>>> Hi James, >>>> >>>> On 1/28/2011 11:00 AM, James Carman wrote: >>>>> >>>>> If I try to run this code on Linux, it fails, but it works on Windows: >>>>> >>>>>> library(affy) >>>>>> aff<- ReadAffy() >>>>>> m5<- mas5(aff) >>>>> >>>>> background correction: mas >>>>> PM/MM correction : mas >>>>> expression values: mas >>>>> background correcting...Error in as.vector(data) : NAs in foreign >>>>> function call (arg 2) >>>> >>>> Let's start with something simple. Can you run mas5() on the Dilution >>>> data >>>> from the affydata package? I get >>>> >>>>> library(affydata) >>>> >>>> Loading required package: affy >>>> Loading required package: Biobase >>>> >>>> Welcome to Bioconductor >>>> >>>> Vignettes contain introductory material. To view, type >>>> 'openVignette()'. To cite Bioconductor, see >>>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>>> >>>>> data(Dilution) >>>>> m5<- mas5(Dilution) >>>> >>>> background correction: mas >>>> PM/MM correction : mas >>>> expression values: mas >>>> background correcting...done. >>>> 12625 ids to be processed >>>> | | >>>> |####################| >>>>> >>>>> sessionInfo() >>>> >>>> R version 2.12.0 beta (2010-09-30 r53083) >>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 >>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915 >>>> [7] LC_PAPER=en_US.iso885915 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] hgu95av2cdf_2.7.0 affydata_1.11.10 affy_1.28.0 Biobase_2.10.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.0 >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>>> >>>>> Here's the result of sessionInfo(): >>>>>> >>>>>> sessionInfo() >>>>> >>>>> R version 2.12.1 (2010-12-16) >>>>> Platform: x86_64-redhat-linux-gnu (64-bit) >>>>> >>>>> locale: >>>>> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C >>>>> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 >>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 >>>>> [7] LC_PAPER=en_US.utf8 LC_NAME=C >>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] hgu133a2cdf_2.7.0 affy_1.28.0 Biobase_2.10.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] affyio_1.16.0 preprocessCore_1.10.0 tools_2.12.1 >>>>> >>>>> Here's my platform: >>>>> >>>>>> uname -a >>>>> >>>>> Linux carman-op755 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23 16:04:50 >>>>> UTC 2010 x86_64 x86_64 x86_64 GNU/Linux >>>>> >>>>> Here's the version of R that I'm running: >>>>> >>>>>> rpm -qa | grep R- >>>>> >>>>> R-core-2.12.1-1.fc14.x86_64 >>>>> R-devel-2.12.1-1.fc14.x86_64 >>>>> R-2.12.1-1.fc14.x86_64 >>>>> >>>>> >>>>> We have used this process in the past and it has worked fine. I got a >>>>> new computer and installed the latest Bioconductor package(s) on it >>>>> and now I'm getting this failure. Any ideas? >>>>> >>>>> Thank you, >>>>> >>>>> James Carman >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> Douglas Lab >>>> University of Michigan >>>> Department of Human Genetics >>>> 5912 Buhl >>>> 1241 E. Catherine St. >>>> Ann Arbor MI 48109-5618 >>>> 734-615-7826 >>>> ********************************************************** >>>> Electronic Mail is not secure, may not be read every day, and should not >>>> be >>>> used for urgent or sensitive issues >>>> >>> >>> _______________________________________________ >>> 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 >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> > > _______________________________________________ > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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> traceback() 10: .C("affy_background_adjust_R", as.double(as.vector(allintensities)), as.integer(allx), as.integer(ally), as.integer(nprobes), as.integer(nchips), as.integer(rows), as.integer(cols), as.integer(griddim), PACKAGE = "affy") 9: as.vector(data) 8: matrix(.C("affy_background_adjust_R", as.double(as.vector(allintensities)), as.integer(allx), as.integer(ally), as.integer(nprobes), as.integer(nchips), as.integer(rows), as.integer(cols), as.integer(griddim), PACKAGE = "affy")[[1]], nprobes, nchips) 7: bg.correct.mas(object, ...) 6: do.call(methodname, alist(object, ...)) 5: function (object, method, ...) standardGeneric("bg.correct")(afbatch, method = bgcorrect.method) 4: function (object, method, ...) standardGeneric("bg.correct")(afbatch, method = bgcorrect.method) 3: do.call(affy:::bg.correct, c(alist(afbatch, method = bgcorrect.method), bgcorrect.param)) 2: expresso(object, bgcorrect.method = "mas", pmcorrect.method = "mas", normalize = FALSE, summary.method = "mas", ...) 1: mas5(aff) On Fri, Jan 28, 2011 at 1:04 PM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > What do you get from traceback()? > > On 1/28/2011 12:47 PM, James Carman wrote: >> >> I tried what you recommended: >> >>> library(affy) >> >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> ? Vignettes contain introductory material. To view, type >> ? 'openVignette()'. To cite Bioconductor, see >> ? 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >>> aff = ReadAffy() >>> anyis.na(exprs(aff))) >> >> [1] FALSE >>> >>> m5 = mas5(aff) >> >> background correction: mas >> PM/MM correction : mas >> expression values: mas >> background correcting...Error in as.vector(data) : NAs in foreign >> function call (arg 2) >> >> So, no NA values in my data. >> >> On Fri, Jan 28, 2011 at 12:41 PM, James W. MacDonald >> <jmacdon at="" med.umich.edu=""> ?wrote: >>> >>> On 1/28/2011 11:47 AM, James Carman wrote: >>>> >>>> Looks like that worked for me (after it downloaded hgu95av2cdf of >>>> course). ?So, what does that mean? >>> >>> It means there isn't any weird Linux/mas5() interaction going on, so we >>> can >>> look at your data. The error you report indicates you have some NA values >>> in >>> your data somewhere. So the first step is to check. >>> >>> anyis.na(exprs(aff))) >>> >>> This should return TRUE. If so, you can track it down to the 'bad' >>> celfile >>> by >>> >>> apply(exprs(aff), 2, function(x) anyis.na(x))) >>> >>> and then try re-uploading that celfile to your Linux box. >>> >>> If not, you can try >>> >>> debug(bg.correct.mas) >>> bg.correct.mas(aff) >>> >>> and step through the function. The error comes at the line >>> >>> ?corrected<- matrix(.C("affy_background_adjust_R", >>> as.double(as.vector(allintensities)), >>> ? ? ? ?as.integer(allx), as.integer(ally), as.integer(nprobes), >>> ? ? ? ?as.integer(nchips), as.integer(rows), as.integer(cols), >>> ? ? ? ?as.integer(griddim), PACKAGE = "affy")[[1]], nprobes, >>> ? ? ? ?nchips) >>> >>> where the data are passed off to a C function. Right before that step you >>> can test the objects 'allx', 'ally' and 'nprobes' for any NA values. Note >>> here that while in the debugger, R shows you the *next* line it is going >>> to >>> interpret, so when you see the above line you can test those objects for >>> the >>> presence of NA values. >>> >>> Let us know what you find! >>> >>> Best, >>> >>> Jim >>> >>> >>> >>> >>> >>>> >>>> On Fri, Jan 28, 2011 at 11:40 AM, James W. MacDonald >>>> <jmacdon at="" med.umich.edu=""> ? ?wrote: >>>>> >>>>> Hi James, >>>>> >>>>> On 1/28/2011 11:00 AM, James Carman wrote: >>>>>> >>>>>> If I try to run this code on Linux, it fails, but it works on Windows: >>>>>> >>>>>>> library(affy) >>>>>>> aff<- ReadAffy() >>>>>>> m5<- mas5(aff) >>>>>> >>>>>> background correction: mas >>>>>> PM/MM correction : mas >>>>>> expression values: mas >>>>>> background correcting...Error in as.vector(data) : NAs in foreign >>>>>> function call (arg 2) >>>>> >>>>> Let's start with something simple. Can you run mas5() on the Dilution >>>>> data >>>>> from the affydata package? I get >>>>> >>>>>> library(affydata) >>>>> >>>>> Loading required package: affy >>>>> Loading required package: Biobase >>>>> >>>>> Welcome to Bioconductor >>>>> >>>>> ?Vignettes contain introductory material. To view, type >>>>> ?'openVignette()'. To cite Bioconductor, see >>>>> ?'citation("Biobase")' and for packages 'citation(pkgname)'. >>>>> >>>>>> data(Dilution) >>>>>> m5<- mas5(Dilution) >>>>> >>>>> background correction: mas >>>>> PM/MM correction : mas >>>>> expression values: mas >>>>> background correcting...done. >>>>> 12625 ids to be processed >>>>> | ? ? ? ? ? ? ? ? ? ?| >>>>> |####################| >>>>>> >>>>>> sessionInfo() >>>>> >>>>> R version 2.12.0 beta (2010-09-30 r53083) >>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>> >>>>> locale: >>>>> ?[1] LC_CTYPE=en_US.iso885915 ? ? ? LC_NUMERIC=C >>>>> ?[3] LC_TIME=en_US.iso885915 ? ? ? ?LC_COLLATE=en_US.iso885915 >>>>> ?[5] LC_MONETARY=C ? ? ? ? ? ? ? ? ?LC_MESSAGES=en_US.iso885915 >>>>> ?[7] LC_PAPER=en_US.iso885915 ? ? ? LC_NAME=C >>>>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? ? ? LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>>> >>>>> other attached packages: >>>>> [1] hgu95av2cdf_2.7.0 affydata_1.11.10 ?affy_1.28.0 >>>>> Biobase_2.10.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] affyio_1.18.0 ? ? ? ? preprocessCore_1.12.0 tools_2.12.0 >>>>> >>>>> Best, >>>>> >>>>> Jim >>>>> >>>>> >>>>>> >>>>>> Here's the result of sessionInfo(): >>>>>>> >>>>>>> sessionInfo() >>>>>> >>>>>> R version 2.12.1 (2010-12-16) >>>>>> Platform: x86_64-redhat-linux-gnu (64-bit) >>>>>> >>>>>> locale: >>>>>> ?[1] LC_CTYPE=en_US.utf8 ? ? ? LC_NUMERIC=C >>>>>> ?[3] LC_TIME=en_US.utf8 ? ? ? ?LC_COLLATE=en_US.utf8 >>>>>> ?[5] LC_MONETARY=C ? ? ? ? ? ? LC_MESSAGES=en_US.utf8 >>>>>> ?[7] LC_PAPER=en_US.utf8 ? ? ? LC_NAME=C >>>>>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ?LC_TELEPHONE=C >>>>>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C >>>>>> >>>>>> attached base packages: >>>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>>>> >>>>>> other attached packages: >>>>>> [1] hgu133a2cdf_2.7.0 affy_1.28.0 ? ? ? Biobase_2.10.0 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] affyio_1.16.0 ? ? ? ? preprocessCore_1.10.0 tools_2.12.1 >>>>>> >>>>>> Here's my platform: >>>>>> >>>>>>> uname -a >>>>>> >>>>>> Linux carman-op755 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23 16:04:50 >>>>>> UTC 2010 x86_64 x86_64 x86_64 GNU/Linux >>>>>> >>>>>> Here's the version of R that I'm running: >>>>>> >>>>>>> rpm -qa | grep R- >>>>>> >>>>>> R-core-2.12.1-1.fc14.x86_64 >>>>>> R-devel-2.12.1-1.fc14.x86_64 >>>>>> R-2.12.1-1.fc14.x86_64 >>>>>> >>>>>> >>>>>> We have used this process in the past and it has worked fine. ?I got a >>>>>> new computer and installed the latest Bioconductor package(s) on it >>>>>> and now I'm getting this failure. ?Any ideas? >>>>>> >>>>>> Thank you, >>>>>> >>>>>> James Carman >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> Douglas Lab >>>>> University of Michigan >>>>> Department of Human Genetics >>>>> 5912 Buhl >>>>> 1241 E. Catherine St. >>>>> Ann Arbor MI 48109-5618 >>>>> 734-615-7826 >>>>> ********************************************************** >>>>> Electronic Mail is not secure, may not be read every day, and should >>>>> not >>>>> be >>>>> used for urgent or sensitive issues >>>>> >>>> >>>> _______________________________________________ >>>> 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 >>> Douglas Lab >>> University of Michigan >>> Department of Human Genetics >>> 5912 Buhl >>> 1241 E. Catherine St. >>> Ann Arbor MI 48109-5618 >>> 734-615-7826 >>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and should not >>> be >>> used for urgent or sensitive issues >>> >> >> _______________________________________________ >> 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 > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues >
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So it is as I surmised. Somehow or another you are ending up with NA values in the data passed to the underlying C code. This is 99.9999999% likely to be due to problems with your data, as literally thousands of people have used this function without problems. I don't know how to help you any more than I have. You don't seem interested in running the debugger on bg.correct.mas(), and without any more information than I already know, I am stuck. So unless you are willing to do some work on your end, my best suggestion is to use your Windows box. Best, Jim On 1/28/2011 1:07 PM, James Carman wrote: >> traceback() > 10: .C("affy_background_adjust_R", as.double(as.vector(allintensities)), > as.integer(allx), as.integer(ally), as.integer(nprobes), > as.integer(nchips), as.integer(rows), as.integer(cols), > as.integer(griddim), > PACKAGE = "affy") > 9: as.vector(data) > 8: matrix(.C("affy_background_adjust_R", as.double(as.vector(allintensities)), > as.integer(allx), as.integer(ally), as.integer(nprobes), > as.integer(nchips), as.integer(rows), as.integer(cols), > as.integer(griddim), > PACKAGE = "affy")[[1]], nprobes, nchips) > 7: bg.correct.mas(object, ...) > 6: do.call(methodname, alist(object, ...)) > 5: function (object, method, ...) > standardGeneric("bg.correct")(afbatch, method = bgcorrect.method) > 4: function (object, method, ...) > standardGeneric("bg.correct")(afbatch, method = bgcorrect.method) > 3: do.call(affy:::bg.correct, c(alist(afbatch, method = bgcorrect.method), > bgcorrect.param)) > 2: expresso(object, bgcorrect.method = "mas", pmcorrect.method = "mas", > normalize = FALSE, summary.method = "mas", ...) > 1: mas5(aff) > > > On Fri, Jan 28, 2011 at 1:04 PM, James W. MacDonald > <jmacdon at="" med.umich.edu=""> wrote: >> What do you get from traceback()? >> >> On 1/28/2011 12:47 PM, James Carman wrote: >>> >>> I tried what you recommended: >>> >>>> library(affy) >>> >>> Loading required package: Biobase >>> >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material. To view, type >>> 'openVignette()'. To cite Bioconductor, see >>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>> >>>> aff = ReadAffy() >>>> anyis.na(exprs(aff))) >>> >>> [1] FALSE >>>> >>>> m5 = mas5(aff) >>> >>> background correction: mas >>> PM/MM correction : mas >>> expression values: mas >>> background correcting...Error in as.vector(data) : NAs in foreign >>> function call (arg 2) >>> >>> So, no NA values in my data. >>> >>> On Fri, Jan 28, 2011 at 12:41 PM, James W. MacDonald >>> <jmacdon at="" med.umich.edu=""> wrote: >>>> >>>> On 1/28/2011 11:47 AM, James Carman wrote: >>>>> >>>>> Looks like that worked for me (after it downloaded hgu95av2cdf of >>>>> course). So, what does that mean? >>>> >>>> It means there isn't any weird Linux/mas5() interaction going on, so we >>>> can >>>> look at your data. The error you report indicates you have some NA values >>>> in >>>> your data somewhere. So the first step is to check. >>>> >>>> anyis.na(exprs(aff))) >>>> >>>> This should return TRUE. If so, you can track it down to the 'bad' >>>> celfile >>>> by >>>> >>>> apply(exprs(aff), 2, function(x) anyis.na(x))) >>>> >>>> and then try re-uploading that celfile to your Linux box. >>>> >>>> If not, you can try >>>> >>>> debug(bg.correct.mas) >>>> bg.correct.mas(aff) >>>> >>>> and step through the function. The error comes at the line >>>> >>>> corrected<- matrix(.C("affy_background_adjust_R", >>>> as.double(as.vector(allintensities)), >>>> as.integer(allx), as.integer(ally), as.integer(nprobes), >>>> as.integer(nchips), as.integer(rows), as.integer(cols), >>>> as.integer(griddim), PACKAGE = "affy")[[1]], nprobes, >>>> nchips) >>>> >>>> where the data are passed off to a C function. Right before that step you >>>> can test the objects 'allx', 'ally' and 'nprobes' for any NA values. Note >>>> here that while in the debugger, R shows you the *next* line it is going >>>> to >>>> interpret, so when you see the above line you can test those objects for >>>> the >>>> presence of NA values. >>>> >>>> Let us know what you find! >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>> >>>> >>>> >>>>> >>>>> On Fri, Jan 28, 2011 at 11:40 AM, James W. MacDonald >>>>> <jmacdon at="" med.umich.edu=""> wrote: >>>>>> >>>>>> Hi James, >>>>>> >>>>>> On 1/28/2011 11:00 AM, James Carman wrote: >>>>>>> >>>>>>> If I try to run this code on Linux, it fails, but it works on Windows: >>>>>>> >>>>>>>> library(affy) >>>>>>>> aff<- ReadAffy() >>>>>>>> m5<- mas5(aff) >>>>>>> >>>>>>> background correction: mas >>>>>>> PM/MM correction : mas >>>>>>> expression values: mas >>>>>>> background correcting...Error in as.vector(data) : NAs in foreign >>>>>>> function call (arg 2) >>>>>> >>>>>> Let's start with something simple. Can you run mas5() on the Dilution >>>>>> data >>>>>> from the affydata package? I get >>>>>> >>>>>>> library(affydata) >>>>>> >>>>>> Loading required package: affy >>>>>> Loading required package: Biobase >>>>>> >>>>>> Welcome to Bioconductor >>>>>> >>>>>> Vignettes contain introductory material. To view, type >>>>>> 'openVignette()'. To cite Bioconductor, see >>>>>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>>>>> >>>>>>> data(Dilution) >>>>>>> m5<- mas5(Dilution) >>>>>> >>>>>> background correction: mas >>>>>> PM/MM correction : mas >>>>>> expression values: mas >>>>>> background correcting...done. >>>>>> 12625 ids to be processed >>>>>> | | >>>>>> |####################| >>>>>>> >>>>>>> sessionInfo() >>>>>> >>>>>> R version 2.12.0 beta (2010-09-30 r53083) >>>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>> >>>>>> locale: >>>>>> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C >>>>>> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 >>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915 >>>>>> [7] LC_PAPER=en_US.iso885915 LC_NAME=C >>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >>>>>> >>>>>> attached base packages: >>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] hgu95av2cdf_2.7.0 affydata_1.11.10 affy_1.28.0 >>>>>> Biobase_2.10.0 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.0 >>>>>> >>>>>> Best, >>>>>> >>>>>> Jim >>>>>> >>>>>> >>>>>>> >>>>>>> Here's the result of sessionInfo(): >>>>>>>> >>>>>>>> sessionInfo() >>>>>>> >>>>>>> R version 2.12.1 (2010-12-16) >>>>>>> Platform: x86_64-redhat-linux-gnu (64-bit) >>>>>>> >>>>>>> locale: >>>>>>> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C >>>>>>> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 >>>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 >>>>>>> [7] LC_PAPER=en_US.utf8 LC_NAME=C >>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>>>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C >>>>>>> >>>>>>> attached base packages: >>>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>>> >>>>>>> other attached packages: >>>>>>> [1] hgu133a2cdf_2.7.0 affy_1.28.0 Biobase_2.10.0 >>>>>>> >>>>>>> loaded via a namespace (and not attached): >>>>>>> [1] affyio_1.16.0 preprocessCore_1.10.0 tools_2.12.1 >>>>>>> >>>>>>> Here's my platform: >>>>>>> >>>>>>>> uname -a >>>>>>> >>>>>>> Linux carman-op755 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23 16:04:50 >>>>>>> UTC 2010 x86_64 x86_64 x86_64 GNU/Linux >>>>>>> >>>>>>> Here's the version of R that I'm running: >>>>>>> >>>>>>>> rpm -qa | grep R- >>>>>>> >>>>>>> R-core-2.12.1-1.fc14.x86_64 >>>>>>> R-devel-2.12.1-1.fc14.x86_64 >>>>>>> R-2.12.1-1.fc14.x86_64 >>>>>>> >>>>>>> >>>>>>> We have used this process in the past and it has worked fine. I got a >>>>>>> new computer and installed the latest Bioconductor package(s) on it >>>>>>> and now I'm getting this failure. Any ideas? >>>>>>> >>>>>>> Thank you, >>>>>>> >>>>>>> James Carman >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>> Douglas Lab >>>>>> University of Michigan >>>>>> Department of Human Genetics >>>>>> 5912 Buhl >>>>>> 1241 E. Catherine St. >>>>>> Ann Arbor MI 48109-5618 >>>>>> 734-615-7826 >>>>>> ********************************************************** >>>>>> Electronic Mail is not secure, may not be read every day, and should >>>>>> not >>>>>> be >>>>>> used for urgent or sensitive issues >>>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> Douglas Lab >>>> University of Michigan >>>> Department of Human Genetics >>>> 5912 Buhl >>>> 1241 E. Catherine St. >>>> Ann Arbor MI 48109-5618 >>>> 734-615-7826 >>>> ********************************************************** >>>> Electronic Mail is not secure, may not be read every day, and should not >>>> be >>>> used for urgent or sensitive issues >>>> >>> >>> _______________________________________________ >>> 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 >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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<snip> >>>>>>>>> sessionInfo() >>>>>>>> >>>>>>>> R version 2.12.1 (2010-12-16) >>>>>>>> Platform: x86_64-redhat-linux-gnu (64-bit) >>>>>>>> >>>>>>>> locale: >>>>>>>> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C >>>>>>>> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 >>>>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 >>>>>>>> [7] LC_PAPER=en_US.utf8 LC_NAME=C >>>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>>>>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C >>>>>>>> >>>>>>>> attached base packages: >>>>>>>> [1] stats graphics grDevices utils datasets methods >>>>>>>> base >>>>>>>> >>>>>>>> other attached packages: >>>>>>>> [1] hgu133a2cdf_2.7.0 affy_1.28.0 Biobase_2.10.0 >>>>>>>> >>>>>>>> loaded via a namespace (and not attached): >>>>>>>> [1] affyio_1.16.0 preprocessCore_1.10.0 tools_2.12.1 uh oh! I get > sessionInfo() R version 2.12.0 Patched (2010-11-28 r53696) 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=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 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] affy_1.28.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.0 and see, e.g., affyio 1.18.0 on the Bioc web site http://bioconductor.org/help/bioc-views/release/bioc/html/affyio.html so the first thing is to update packages as at http://bioconductor.org/install/index.html#update-bioconductor- packages Martin >>>>>>>> >>>>>>>> Here's my platform: >>>>>>>> >>>>>>>>> uname -a >>>>>>>> >>>>>>>> Linux carman-op755 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23 >>>>>>>> 16:04:50 >>>>>>>> UTC 2010 x86_64 x86_64 x86_64 GNU/Linux >>>>>>>> >>>>>>>> Here's the version of R that I'm running: >>>>>>>> >>>>>>>>> rpm -qa | grep R- >>>>>>>> >>>>>>>> R-core-2.12.1-1.fc14.x86_64 >>>>>>>> R-devel-2.12.1-1.fc14.x86_64 >>>>>>>> R-2.12.1-1.fc14.x86_64 >>>>>>>> >>>>>>>> >>>>>>>> We have used this process in the past and it has worked fine. I >>>>>>>> got a >>>>>>>> new computer and installed the latest Bioconductor package(s) on it >>>>>>>> and now I'm getting this failure. Any ideas? >>>>>>>> >>>>>>>> Thank you, >>>>>>>> >>>>>>>> James Carman >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>>>>> Douglas Lab >>>>>>> University of Michigan >>>>>>> Department of Human Genetics >>>>>>> 5912 Buhl >>>>>>> 1241 E. Catherine St. >>>>>>> Ann Arbor MI 48109-5618 >>>>>>> 734-615-7826 >>>>>>> ********************************************************** >>>>>>> Electronic Mail is not secure, may not be read every day, and should >>>>>>> not >>>>>>> be >>>>>>> used for urgent or sensitive issues >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> Douglas Lab >>>>> University of Michigan >>>>> Department of Human Genetics >>>>> 5912 Buhl >>>>> 1241 E. Catherine St. >>>>> Ann Arbor MI 48109-5618 >>>>> 734-615-7826 >>>>> ********************************************************** >>>>> Electronic Mail is not secure, may not be read every day, and >>>>> should not >>>>> be >>>>> used for urgent or sensitive issues >>>>> >>>> >>>> _______________________________________________ >>>> 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 >>> Douglas Lab >>> University of Michigan >>> Department of Human Genetics >>> 5912 Buhl >>> 1241 E. Catherine St. >>> Ann Arbor MI 48109-5618 >>> 734-615-7826 >>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and should >>> not be >>> used for urgent or sensitive issues >>> > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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Ding, dong, the witch is dead! Thank you Martin! I just did: source("http://bioconductor.org/biocLite.R") biocLite("affyio") and it updated the "affyio" package. Then I tried again and all seems to be working. So, I don't have to do debugging after all! WHEW! :) Thank you guys for all your help. Now, if anyone has any R book suggestions, I'm all ears! On Fri, Jan 28, 2011 at 2:50 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > <snip> > >>>>>>>>>> sessionInfo() >>>>>>>>> >>>>>>>>> R version 2.12.1 (2010-12-16) >>>>>>>>> Platform: x86_64-redhat-linux-gnu (64-bit) >>>>>>>>> >>>>>>>>> locale: >>>>>>>>> ? [1] LC_CTYPE=en_US.utf8 ? ? ? LC_NUMERIC=C >>>>>>>>> ? [3] LC_TIME=en_US.utf8 ? ? ? ?LC_COLLATE=en_US.utf8 >>>>>>>>> ? [5] LC_MONETARY=C ? ? ? ? ? ? LC_MESSAGES=en_US.utf8 >>>>>>>>> ? [7] LC_PAPER=en_US.utf8 ? ? ? LC_NAME=C >>>>>>>>> ? [9] LC_ADDRESS=C ? ? ? ? ? ? ?LC_TELEPHONE=C >>>>>>>>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C >>>>>>>>> >>>>>>>>> attached base packages: >>>>>>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods >>>>>>>>> base >>>>>>>>> >>>>>>>>> other attached packages: >>>>>>>>> [1] hgu133a2cdf_2.7.0 affy_1.28.0 ? ? ? Biobase_2.10.0 >>>>>>>>> >>>>>>>>> loaded via a namespace (and not attached): >>>>>>>>> [1] affyio_1.16.0 ? ? ? ? preprocessCore_1.10.0 tools_2.12.1 > > uh oh! I get > >> sessionInfo() > R version 2.12.0 Patched (2010-11-28 r53696) > 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=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 > ?[7] LC_PAPER=en_US.UTF-8 ? ? ? 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] affy_1.28.0 ? ?Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 ? ? ? ? preprocessCore_1.12.0 tools_2.12.0 > > and see, e.g., affyio 1.18.0 on the Bioc web site > > http://bioconductor.org/help/bioc- views/release/bioc/html/affyio.html > > so the first thing is to update packages as at > > http://bioconductor.org/install/index.html#update-bioconductor- packages > > Martin > >>>>>>>>> >>>>>>>>> Here's my platform: >>>>>>>>> >>>>>>>>>> uname -a >>>>>>>>> >>>>>>>>> Linux carman-op755 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23 >>>>>>>>> 16:04:50 >>>>>>>>> UTC 2010 x86_64 x86_64 x86_64 GNU/Linux >>>>>>>>> >>>>>>>>> Here's the version of R that I'm running: >>>>>>>>> >>>>>>>>>> rpm -qa | grep R- >>>>>>>>> >>>>>>>>> R-core-2.12.1-1.fc14.x86_64 >>>>>>>>> R-devel-2.12.1-1.fc14.x86_64 >>>>>>>>> R-2.12.1-1.fc14.x86_64 >>>>>>>>> >>>>>>>>> >>>>>>>>> We have used this process in the past and it has worked fine. ?I >>>>>>>>> got a >>>>>>>>> new computer and installed the latest Bioconductor package(s) on it >>>>>>>>> and now I'm getting this failure. ?Any ideas? >>>>>>>>> >>>>>>>>> Thank you, >>>>>>>>> >>>>>>>>> James Carman >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> 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 >>>>>>>> Douglas Lab >>>>>>>> University of Michigan >>>>>>>> Department of Human Genetics >>>>>>>> 5912 Buhl >>>>>>>> 1241 E. Catherine St. >>>>>>>> Ann Arbor MI 48109-5618 >>>>>>>> 734-615-7826 >>>>>>>> ********************************************************** >>>>>>>> Electronic Mail is not secure, may not be read every day, and should >>>>>>>> not >>>>>>>> be >>>>>>>> used for urgent or sensitive issues >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>> Douglas Lab >>>>>> University of Michigan >>>>>> Department of Human Genetics >>>>>> 5912 Buhl >>>>>> 1241 E. Catherine St. >>>>>> Ann Arbor MI 48109-5618 >>>>>> 734-615-7826 >>>>>> ********************************************************** >>>>>> Electronic Mail is not secure, may not be read every day, and >>>>>> should not >>>>>> be >>>>>> used for urgent or sensitive issues >>>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> Douglas Lab >>>> University of Michigan >>>> Department of Human Genetics >>>> 5912 Buhl >>>> 1241 E. Catherine St. >>>> Ann Arbor MI 48109-5618 >>>> 734-615-7826 >>>> ********************************************************** >>>> Electronic Mail is not secure, may not be read every day, and should >>>> not be >>>> used for urgent or sensitive issues >>>> >> > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 >
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On 01/28/2011 11:54 AM, James Carman wrote: > Ding, dong, the witch is dead! Thank you Martin! I just did: > > source("http://bioconductor.org/biocLite.R") > biocLite("affyio") You want to follow the instructions for updating packages, not installing a particular one; likely you have a Frankenstein system at the moment. In a new R source('http://bioconductor.org/biocLite.R') update.packages(repos=biocinstallRepos(), ask=FALSE) or a recently learned (for me) and probably better approach options(repos=c(CRAN="http://cran.fhrcr.org")) setRepositories() ## select CRAN and all BioC old.packages() ## to see what you are saving yourself from... update.packages(ask=FALSE) In terms of books from a developer perspective (rather than 'using R' or 'bioinformatic analysis') I'm partial to Chambers' Software for Data Analysis and Gentleman's R Programming for Bioinformatics. Martin > > and it updated the "affyio" package. Then I tried again and all seems > to be working. So, I don't have to do debugging after all! WHEW! :) > Thank you guys for all your help. Now, if anyone has any R book > suggestions, I'm all ears! > > On Fri, Jan 28, 2011 at 2:50 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: >> <snip> >> >>>>>>>>>>> sessionInfo() >>>>>>>>>> >>>>>>>>>> R version 2.12.1 (2010-12-16) >>>>>>>>>> Platform: x86_64-redhat-linux-gnu (64-bit) >>>>>>>>>> >>>>>>>>>> locale: >>>>>>>>>> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C >>>>>>>>>> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 >>>>>>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 >>>>>>>>>> [7] LC_PAPER=en_US.utf8 LC_NAME=C >>>>>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>>>>>>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C >>>>>>>>>> >>>>>>>>>> attached base packages: >>>>>>>>>> [1] stats graphics grDevices utils datasets methods >>>>>>>>>> base >>>>>>>>>> >>>>>>>>>> other attached packages: >>>>>>>>>> [1] hgu133a2cdf_2.7.0 affy_1.28.0 Biobase_2.10.0 >>>>>>>>>> >>>>>>>>>> loaded via a namespace (and not attached): >>>>>>>>>> [1] affyio_1.16.0 preprocessCore_1.10.0 tools_2.12.1 >> >> uh oh! I get >> >>> sessionInfo() >> R version 2.12.0 Patched (2010-11-28 r53696) >> 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=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 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] affy_1.28.0 Biobase_2.10.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.0 >> >> and see, e.g., affyio 1.18.0 on the Bioc web site >> >> http://bioconductor.org/help/bioc- views/release/bioc/html/affyio.html >> >> so the first thing is to update packages as at >> >> http://bioconductor.org/install/index.html#update-bioconductor- packages >> >> Martin >> >>>>>>>>>> >>>>>>>>>> Here's my platform: >>>>>>>>>> >>>>>>>>>>> uname -a >>>>>>>>>> >>>>>>>>>> Linux carman-op755 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23 >>>>>>>>>> 16:04:50 >>>>>>>>>> UTC 2010 x86_64 x86_64 x86_64 GNU/Linux >>>>>>>>>> >>>>>>>>>> Here's the version of R that I'm running: >>>>>>>>>> >>>>>>>>>>> rpm -qa | grep R- >>>>>>>>>> >>>>>>>>>> R-core-2.12.1-1.fc14.x86_64 >>>>>>>>>> R-devel-2.12.1-1.fc14.x86_64 >>>>>>>>>> R-2.12.1-1.fc14.x86_64 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> We have used this process in the past and it has worked fine. I >>>>>>>>>> got a >>>>>>>>>> new computer and installed the latest Bioconductor package(s) on it >>>>>>>>>> and now I'm getting this failure. Any ideas? >>>>>>>>>> >>>>>>>>>> Thank you, >>>>>>>>>> >>>>>>>>>> James Carman >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> 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 >>>>>>>>> Douglas Lab >>>>>>>>> University of Michigan >>>>>>>>> Department of Human Genetics >>>>>>>>> 5912 Buhl >>>>>>>>> 1241 E. Catherine St. >>>>>>>>> Ann Arbor MI 48109-5618 >>>>>>>>> 734-615-7826 >>>>>>>>> ********************************************************** >>>>>>>>> Electronic Mail is not secure, may not be read every day, and should >>>>>>>>> not >>>>>>>>> be >>>>>>>>> used for urgent or sensitive issues >>>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>>>>> Douglas Lab >>>>>>> University of Michigan >>>>>>> Department of Human Genetics >>>>>>> 5912 Buhl >>>>>>> 1241 E. Catherine St. >>>>>>> Ann Arbor MI 48109-5618 >>>>>>> 734-615-7826 >>>>>>> ********************************************************** >>>>>>> Electronic Mail is not secure, may not be read every day, and >>>>>>> should not >>>>>>> be >>>>>>> used for urgent or sensitive issues >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> Douglas Lab >>>>> University of Michigan >>>>> Department of Human Genetics >>>>> 5912 Buhl >>>>> 1241 E. Catherine St. >>>>> Ann Arbor MI 48109-5618 >>>>> 734-615-7826 >>>>> ********************************************************** >>>>> Electronic Mail is not secure, may not be read every day, and should >>>>> not be >>>>> used for urgent or sensitive issues >>>>> >>> >> >> >> -- >> Computational Biology >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >> >> Location: M1-B861 >> Telephone: 206 667-2793 >> -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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On Fri, Jan 28, 2011 at 3:01 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > > You want to follow the instructions for updating packages, not > installing a particular one; likely you have a Frankenstein system at > the moment. In a new R > > source('http://bioconductor.org/biocLite.R') > update.packages(repos=biocinstallRepos(), ask=FALSE) > I went with this approach, since this is what the Bioconductor folks have on their site. > or a recently learned (for me) and probably better approach > > options(repos=c(CRAN="http://cran.fhrcr.org")) > setRepositories() ?## select CRAN and all BioC > old.packages() ?## to see what you are saving yourself from... > update.packages(ask=FALSE) > This looked a bit scary to me with the hard-coded server name in there, so I went with the other way. :) > In terms of books from a developer perspective (rather than 'using R' or > 'bioinformatic analysis') I'm partial to Chambers' Software for Data > Analysis and Gentleman's R Programming for Bioinformatics. > Cool, thanks! These books are a bit old. Is there any reason to worry about that? Has the information become obsolete at all? Has R changed that much in the past 2-3 years?
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On 1/28/2011 3:23 PM, James Carman wrote: > On Fri, Jan 28, 2011 at 3:01 PM, Martin Morgan<mtmorgan at="" fhcrc.org=""> wrote: >> >> You want to follow the instructions for updating packages, not >> installing a particular one; likely you have a Frankenstein system at >> the moment. In a new R >> >> source('http://bioconductor.org/biocLite.R') >> update.packages(repos=biocinstallRepos(), ask=FALSE) >> > > I went with this approach, since this is what the Bioconductor folks > have on their site. > >> or a recently learned (for me) and probably better approach >> >> options(repos=c(CRAN="http://cran.fhrcr.org")) >> setRepositories() ## select CRAN and all BioC >> old.packages() ## to see what you are saving yourself from... >> update.packages(ask=FALSE) >> > > This looked a bit scary to me with the hard-coded server name in > there, so I went with the other way. :) > >> In terms of books from a developer perspective (rather than 'using R' or >> 'bioinformatic analysis') I'm partial to Chambers' Software for Data >> Analysis and Gentleman's R Programming for Bioinformatics. >> > > Cool, thanks! These books are a bit old. Is there any reason to > worry about that? Has the information become obsolete at all? Has R > changed that much in the past 2-3 years? Not so much that either book is obsolete. Maybe Amazon has both together for a good deal ;-D -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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I'm willing to do some work. I'm just a bit green when it comes to R, so your requests were a bit daunting at first. Your instructions seem thorough enough, though. So, perhaps I'll try it out. For right now, I've just turned off background correction and I'm getting all of my downstream processing stuff working with the resulting data from that. However, we definitely need background correction, so I need to fix this issue. I thank you for being so helpful. I'll report back what I find or if I have further questions. Anyone have any good suggestions as far as books on R are concerned? I need to get a good tutorial/reference book. I'm a Java guy, but have been asked to do this R stuff by my client, so I'm trying to blindly feel my way around. On Fri, Jan 28, 2011 at 2:39 PM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > So it is as I surmised. Somehow or another you are ending up with NA values > in the data passed to the underlying C code. This is 99.9999999% likely to > be due to problems with your data, as literally thousands of people have > used this function without problems. > > I don't know how to help you any more than I have. You don't seem interested > in running the debugger on bg.correct.mas(), and without any more > information than I already know, I am stuck. > > So unless you are willing to do some work on your end, my best suggestion is > to use your Windows box. > > Best, > > Jim > > > > On 1/28/2011 1:07 PM, James Carman wrote: >>> >>> traceback() >> >> 10: .C("affy_background_adjust_R", as.double(as.vector(allintensities)), >> ? ? ? ? as.integer(allx), as.integer(ally), as.integer(nprobes), >> ? ? ? ? as.integer(nchips), as.integer(rows), as.integer(cols), >> as.integer(griddim), >> ? ? ? ? PACKAGE = "affy") >> 9: as.vector(data) >> 8: matrix(.C("affy_background_adjust_R", >> as.double(as.vector(allintensities)), >> ? ? ? ?as.integer(allx), as.integer(ally), as.integer(nprobes), >> ? ? ? ?as.integer(nchips), as.integer(rows), as.integer(cols), >> as.integer(griddim), >> ? ? ? ?PACKAGE = "affy")[[1]], nprobes, nchips) >> 7: bg.correct.mas(object, ...) >> 6: do.call(methodname, alist(object, ...)) >> 5: function (object, method, ...) >> ? ?standardGeneric("bg.correct")(afbatch, method = bgcorrect.method) >> 4: function (object, method, ...) >> ? ?standardGeneric("bg.correct")(afbatch, method = bgcorrect.method) >> 3: do.call(affy:::bg.correct, c(alist(afbatch, method = bgcorrect.method), >> ? ? ? ?bgcorrect.param)) >> 2: expresso(object, bgcorrect.method = "mas", pmcorrect.method = "mas", >> ? ? ? ?normalize = FALSE, summary.method = "mas", ...) >> 1: mas5(aff) >> >> >> On Fri, Jan 28, 2011 at 1:04 PM, James W. MacDonald >> <jmacdon at="" med.umich.edu=""> ?wrote: >>> >>> What do you get from traceback()? >>> >>> On 1/28/2011 12:47 PM, James Carman wrote: >>>> >>>> I tried what you recommended: >>>> >>>>> library(affy) >>>> >>>> Loading required package: Biobase >>>> >>>> Welcome to Bioconductor >>>> >>>> ? Vignettes contain introductory material. To view, type >>>> ? 'openVignette()'. To cite Bioconductor, see >>>> ? 'citation("Biobase")' and for packages 'citation(pkgname)'. >>>> >>>>> aff = ReadAffy() >>>>> anyis.na(exprs(aff))) >>>> >>>> [1] FALSE >>>>> >>>>> m5 = mas5(aff) >>>> >>>> background correction: mas >>>> PM/MM correction : mas >>>> expression values: mas >>>> background correcting...Error in as.vector(data) : NAs in foreign >>>> function call (arg 2) >>>> >>>> So, no NA values in my data. >>>> >>>> On Fri, Jan 28, 2011 at 12:41 PM, James W. MacDonald >>>> <jmacdon at="" med.umich.edu=""> ? ?wrote: >>>>> >>>>> On 1/28/2011 11:47 AM, James Carman wrote: >>>>>> >>>>>> Looks like that worked for me (after it downloaded hgu95av2cdf of >>>>>> course). ?So, what does that mean? >>>>> >>>>> It means there isn't any weird Linux/mas5() interaction going on, so we >>>>> can >>>>> look at your data. The error you report indicates you have some NA >>>>> values >>>>> in >>>>> your data somewhere. So the first step is to check. >>>>> >>>>> anyis.na(exprs(aff))) >>>>> >>>>> This should return TRUE. If so, you can track it down to the 'bad' >>>>> celfile >>>>> by >>>>> >>>>> apply(exprs(aff), 2, function(x) anyis.na(x))) >>>>> >>>>> and then try re-uploading that celfile to your Linux box. >>>>> >>>>> If not, you can try >>>>> >>>>> debug(bg.correct.mas) >>>>> bg.correct.mas(aff) >>>>> >>>>> and step through the function. The error comes at the line >>>>> >>>>> ?corrected<- matrix(.C("affy_background_adjust_R", >>>>> as.double(as.vector(allintensities)), >>>>> ? ? ? ?as.integer(allx), as.integer(ally), as.integer(nprobes), >>>>> ? ? ? ?as.integer(nchips), as.integer(rows), as.integer(cols), >>>>> ? ? ? ?as.integer(griddim), PACKAGE = "affy")[[1]], nprobes, >>>>> ? ? ? ?nchips) >>>>> >>>>> where the data are passed off to a C function. Right before that step >>>>> you >>>>> can test the objects 'allx', 'ally' and 'nprobes' for any NA values. >>>>> Note >>>>> here that while in the debugger, R shows you the *next* line it is >>>>> going >>>>> to >>>>> interpret, so when you see the above line you can test those objects >>>>> for >>>>> the >>>>> presence of NA values. >>>>> >>>>> Let us know what you find! >>>>> >>>>> Best, >>>>> >>>>> Jim >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>> >>>>>> On Fri, Jan 28, 2011 at 11:40 AM, James W. MacDonald >>>>>> <jmacdon at="" med.umich.edu=""> ? ? ?wrote: >>>>>>> >>>>>>> Hi James, >>>>>>> >>>>>>> On 1/28/2011 11:00 AM, James Carman wrote: >>>>>>>> >>>>>>>> If I try to run this code on Linux, it fails, but it works on >>>>>>>> Windows: >>>>>>>> >>>>>>>>> library(affy) >>>>>>>>> aff<- ReadAffy() >>>>>>>>> m5<- mas5(aff) >>>>>>>> >>>>>>>> background correction: mas >>>>>>>> PM/MM correction : mas >>>>>>>> expression values: mas >>>>>>>> background correcting...Error in as.vector(data) : NAs in foreign >>>>>>>> function call (arg 2) >>>>>>> >>>>>>> Let's start with something simple. Can you run mas5() on the Dilution >>>>>>> data >>>>>>> from the affydata package? I get >>>>>>> >>>>>>>> library(affydata) >>>>>>> >>>>>>> Loading required package: affy >>>>>>> Loading required package: Biobase >>>>>>> >>>>>>> Welcome to Bioconductor >>>>>>> >>>>>>> ?Vignettes contain introductory material. To view, type >>>>>>> ?'openVignette()'. To cite Bioconductor, see >>>>>>> ?'citation("Biobase")' and for packages 'citation(pkgname)'. >>>>>>> >>>>>>>> data(Dilution) >>>>>>>> m5<- mas5(Dilution) >>>>>>> >>>>>>> background correction: mas >>>>>>> PM/MM correction : mas >>>>>>> expression values: mas >>>>>>> background correcting...done. >>>>>>> 12625 ids to be processed >>>>>>> | ? ? ? ? ? ? ? ? ? ?| >>>>>>> |####################| >>>>>>>> >>>>>>>> sessionInfo() >>>>>>> >>>>>>> R version 2.12.0 beta (2010-09-30 r53083) >>>>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>>> >>>>>>> locale: >>>>>>> ?[1] LC_CTYPE=en_US.iso885915 ? ? ? LC_NUMERIC=C >>>>>>> ?[3] LC_TIME=en_US.iso885915 ? ? ? ?LC_COLLATE=en_US.iso885915 >>>>>>> ?[5] LC_MONETARY=C ? ? ? ? ? ? ? ? ?LC_MESSAGES=en_US.iso885915 >>>>>>> ?[7] LC_PAPER=en_US.iso885915 ? ? ? LC_NAME=C >>>>>>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? ? ? LC_TELEPHONE=C >>>>>>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >>>>>>> >>>>>>> attached base packages: >>>>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>>>>> >>>>>>> other attached packages: >>>>>>> [1] hgu95av2cdf_2.7.0 affydata_1.11.10 ?affy_1.28.0 >>>>>>> Biobase_2.10.0 >>>>>>> >>>>>>> loaded via a namespace (and not attached): >>>>>>> [1] affyio_1.18.0 ? ? ? ? preprocessCore_1.12.0 tools_2.12.0 >>>>>>> >>>>>>> Best, >>>>>>> >>>>>>> Jim >>>>>>> >>>>>>> >>>>>>>> >>>>>>>> Here's the result of sessionInfo(): >>>>>>>>> >>>>>>>>> sessionInfo() >>>>>>>> >>>>>>>> R version 2.12.1 (2010-12-16) >>>>>>>> Platform: x86_64-redhat-linux-gnu (64-bit) >>>>>>>> >>>>>>>> locale: >>>>>>>> ?[1] LC_CTYPE=en_US.utf8 ? ? ? LC_NUMERIC=C >>>>>>>> ?[3] LC_TIME=en_US.utf8 ? ? ? ?LC_COLLATE=en_US.utf8 >>>>>>>> ?[5] LC_MONETARY=C ? ? ? ? ? ? LC_MESSAGES=en_US.utf8 >>>>>>>> ?[7] LC_PAPER=en_US.utf8 ? ? ? LC_NAME=C >>>>>>>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ?LC_TELEPHONE=C >>>>>>>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C >>>>>>>> >>>>>>>> attached base packages: >>>>>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>>>>>> >>>>>>>> other attached packages: >>>>>>>> [1] hgu133a2cdf_2.7.0 affy_1.28.0 ? ? ? Biobase_2.10.0 >>>>>>>> >>>>>>>> loaded via a namespace (and not attached): >>>>>>>> [1] affyio_1.16.0 ? ? ? ? preprocessCore_1.10.0 tools_2.12.1 >>>>>>>> >>>>>>>> Here's my platform: >>>>>>>> >>>>>>>>> uname -a >>>>>>>> >>>>>>>> Linux carman-op755 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23 >>>>>>>> 16:04:50 >>>>>>>> UTC 2010 x86_64 x86_64 x86_64 GNU/Linux >>>>>>>> >>>>>>>> Here's the version of R that I'm running: >>>>>>>> >>>>>>>>> rpm -qa | grep R- >>>>>>>> >>>>>>>> R-core-2.12.1-1.fc14.x86_64 >>>>>>>> R-devel-2.12.1-1.fc14.x86_64 >>>>>>>> R-2.12.1-1.fc14.x86_64 >>>>>>>> >>>>>>>> >>>>>>>> We have used this process in the past and it has worked fine. ?I got >>>>>>>> a >>>>>>>> new computer and installed the latest Bioconductor package(s) on it >>>>>>>> and now I'm getting this failure. ?Any ideas? >>>>>>>> >>>>>>>> Thank you, >>>>>>>> >>>>>>>> James Carman >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>>>>> Douglas Lab >>>>>>> University of Michigan >>>>>>> Department of Human Genetics >>>>>>> 5912 Buhl >>>>>>> 1241 E. Catherine St. >>>>>>> Ann Arbor MI 48109-5618 >>>>>>> 734-615-7826 >>>>>>> ********************************************************** >>>>>>> Electronic Mail is not secure, may not be read every day, and should >>>>>>> not >>>>>>> be >>>>>>> used for urgent or sensitive issues >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> Douglas Lab >>>>> University of Michigan >>>>> Department of Human Genetics >>>>> 5912 Buhl >>>>> 1241 E. Catherine St. >>>>> Ann Arbor MI 48109-5618 >>>>> 734-615-7826 >>>>> ********************************************************** >>>>> Electronic Mail is not secure, may not be read every day, and should >>>>> not >>>>> be >>>>> used for urgent or sensitive issues >>>>> >>>> >>>> _______________________________________________ >>>> 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 >>> Douglas Lab >>> University of Michigan >>> Department of Human Genetics >>> 5912 Buhl >>> 1241 E. Catherine St. >>> Ann Arbor MI 48109-5618 >>> 734-615-7826 >>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and should not >>> be >>> used for urgent or sensitive issues >>> > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues >
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