matrix row/column displayed as a list
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Daniel Brewer ★ 1.9k
@daniel-brewer-1791
Last seen 10.3 years ago
Hi, This is a silly little question, but I can't find the answer. I have a matrix of expression values e.g. expression. When I display either one column or one row it displays a list e.g. expression[1,] or expression[,1]. Is there a way to change this behaviour? When I constructed a test matrix, the matrix worked as desired i.e. > togo <- matrix(c(1,2,3,4),ncol=2, nrow=2) > togo[,1] [1] 1 2 Why is the behaviour different? Many thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research United Kingdom ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addre...{{dropped}}
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.3 years ago
Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> writes: > Hi, > > This is a silly little question, but I can't find the answer. I have a > matrix of expression values e.g. expression. When I display either one > column or one row it displays a list e.g. expression[1,] or > expression[,1]. Is there a way to change this behaviour? I think you mean that it displays a vector. I think you will find help by reading help("[") and looking at the 'drop' argument. togo <- matrix(c(1,2,3,4),ncol=2, nrow=2) > togo[1, ] [1] 1 3 > togo[1, , drop=FALSE] [,1] [,2] [1,] 1 3 + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.3 years ago
Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> writes: > Yes I have already tried that, class(expression) is matrix. But > class(expression[1,]) is list as is class(expression[,1]). Whereas the > class of my simple constructed matrix when looking at a single row or > column is numeric i.e. class(togo[,2]). > > Thanks for the suggestion anyway. Then you need to provide a lot more detailed information / reproducible example. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
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Hi Duncan and others, I have a problem with saveXML. I'm trying to to this: > saveXML(toGXL(test), file="test.gxl") where 'test' is an object of class graphNEL. This works fine on a linux and PC, but not on mac, which is my standard machine for running R (sessionInfo below). > saveXML(toGXL(test), file="test.gxl") Error in NextMethod("saveXML", object = doc$value()) : no method to invoke > methods(saveXML) [1] saveXML.XMLInternalDOM* saveXML.XMLInternalDocument* saveXML.XMLNode* saveXML.XMLOutputStream* Non-visible functions are asterisked Any ideas? Thanks \Heidi ## MAC ## > sessionInfo() R version 2.4.1 (2006-12-18) i386-apple-darwin8.8.1 locale: en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: geneplotter GOstats Category genefilter survival KEGG RBGL annotate Biobase "1.12.0" "2.0.4" "2.0.3" "1.12.0" "2.30" "1.14.1" "1.10.0" "1.12.1" "1.12.2" GO graph XML "1.14.1" "1.12.1" "1.6-0" ## LINUX ## > sessionInfo() R version 2.5.0 alpha (2007-03-30 r40957) i686-pc-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB .UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: XML GOstats Category AnnotationDbi RSQLite "1.6-2" "2.1.13" "2.1.28" "0.0.56" "0.5-3" DBI Matrix lattice genefilter survival "0.2-1" "0.9975-11" "0.15-1" "1.13.12" "2.31" KEGG RBGL annotate Biobase GO "1.15.13" "1.11.4" "1.13.8" "1.13.44" "1.15.13" graph "1.13.9" ## PC## Don't have the sessionInfo here, but it's back with R2.0 ------------<<>>------------ Heidi Dvinge European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Mail: heidi at ebi.ac.uk Phone: +44 (0) 1223 492 550 ------------<<>>------------
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Hi Heidi This is one is reasonably easy, I hope. You need version 1.6-1 or higher on your Mac. You have it on your Linux machine, but not on your Mac. That may be because you are getting a binary version from a repository and that is not up to date with the releases from the Omegahat site. If you have the compilers installed on your Mac, the R command install.packages("XML", repos = "http://www.omegahat.org/R", type = "source") will get the latest version (1.6-3) and build it. D. hdvi at well.ox.ac.uk wrote: > Hi Duncan and others, > > I have a problem with saveXML. I'm trying to to this: > >> saveXML(toGXL(test), file="test.gxl") > > where 'test' is an object of class graphNEL. This works fine on a linux > and PC, but not on mac, which is my standard machine for running R > (sessionInfo below). > >> saveXML(toGXL(test), file="test.gxl") > Error in NextMethod("saveXML", object = doc$value()) : > no method to invoke >> methods(saveXML) > [1] saveXML.XMLInternalDOM* saveXML.XMLInternalDocument* > saveXML.XMLNode* saveXML.XMLOutputStream* > Non-visible functions are asterisked > > Any ideas? > > Thanks > \Heidi > > ## MAC ## >> sessionInfo() > R version 2.4.1 (2006-12-18) > i386-apple-darwin8.8.1 > > locale: > en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > "datasets" "methods" "base" > > other attached packages: > geneplotter GOstats Category genefilter survival KEGG > RBGL annotate Biobase > "1.12.0" "2.0.4" "2.0.3" "1.12.0" "2.30" "1.14.1" > "1.10.0" "1.12.1" "1.12.2" > GO graph XML > "1.14.1" "1.12.1" "1.6-0" > > ## LINUX ## >> sessionInfo() > R version 2.5.0 alpha (2007-03-30 r40957) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_ GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_G B.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "methods" "base" > > other attached packages: > XML GOstats Category AnnotationDbi RSQLite > "1.6-2" "2.1.13" "2.1.28" "0.0.56" "0.5-3" > DBI Matrix lattice genefilter survival > "0.2-1" "0.9975-11" "0.15-1" "1.13.12" "2.31" > KEGG RBGL annotate Biobase GO > "1.15.13" "1.11.4" "1.13.8" "1.13.44" "1.15.13" > graph > "1.13.9" > > ## PC## > > Don't have the sessionInfo here, but it's back with R2.0 > > ------------<<>>------------ > Heidi Dvinge > > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > Mail: heidi at ebi.ac.uk > Phone: +44 (0) 1223 492 550 > ------------<<>>------------ >
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Hi Duncan, I ran the XML as you specified below, and got version 1.6-2, instead of 1.6-0 which is the CRAN version. When trying the run saveXML the error message persists though. I think it might be a problem with my R installation (R version 2.4.1 (2006-12-18) built from binary), since the function seems to work on another mac (built from source). Also, it worked on a PC, which has an XML version older than the 1.6-0. Haven't had any other problems with R on this mac though. Cheers \Heidi > > Hi Heidi > > This is one is reasonably easy, I hope. > You need version 1.6-1 or higher on your Mac. > You have it on your Linux machine, but not on your Mac. > That may be because you are getting a binary version > from a repository and that is not up to date > with the releases from the Omegahat site. > If you have the compilers installed on your Mac, > the R command > > install.packages("XML", repos = "http://www.omegahat.org/R", > type = "source") > > will get the latest version (1.6-3) and build it. > > D. > > hdvi at well.ox.ac.uk wrote: >> Hi Duncan and others, >> >> I have a problem with saveXML. I'm trying to to this: >> >>> saveXML(toGXL(test), file="test.gxl") >> >> where 'test' is an object of class graphNEL. This works fine on a linux >> and PC, but not on mac, which is my standard machine for running R >> (sessionInfo below). >> >>> saveXML(toGXL(test), file="test.gxl") >> Error in NextMethod("saveXML", object = doc$value()) : >> no method to invoke >>> methods(saveXML) >> [1] saveXML.XMLInternalDOM* saveXML.XMLInternalDocument* >> saveXML.XMLNode* saveXML.XMLOutputStream* >> Non-visible functions are asterisked >> >> Any ideas? >> >> Thanks >> \Heidi >> >> ## MAC ## >>> sessionInfo() >> R version 2.4.1 (2006-12-18) >> i386-apple-darwin8.8.1 >> >> locale: >> en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 >> >> attached base packages: >> [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" >> "datasets" "methods" "base" >> >> other attached packages: >> geneplotter GOstats Category genefilter survival KEGG >> RBGL annotate Biobase >> "1.12.0" "2.0.4" "2.0.3" "1.12.0" "2.30" "1.14.1" >> "1.10.0" "1.12.1" "1.12.2" >> GO graph XML >> "1.14.1" "1.12.1" "1.6-0" >> >> ## LINUX ## >>> sessionInfo() >> R version 2.5.0 alpha (2007-03-30 r40957) >> i686-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en _GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_ GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UT F-8;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" >> [7] "datasets" "methods" "base" >> >> other attached packages: >> XML GOstats Category AnnotationDbi RSQLite >> "1.6-2" "2.1.13" "2.1.28" "0.0.56" "0.5-3" >> DBI Matrix lattice genefilter survival >> "0.2-1" "0.9975-11" "0.15-1" "1.13.12" "2.31" >> KEGG RBGL annotate Biobase GO >> "1.15.13" "1.11.4" "1.13.8" "1.13.44" "1.15.13" >> graph >> "1.13.9" >> >> ## PC## >> >> Don't have the sessionInfo here, but it's back with R2.0 >> >> ------------<<>>------------ >> Heidi Dvinge >> >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> Mail: heidi at ebi.ac.uk >> Phone: +44 (0) 1223 492 550 >> ------------<<>>------------ >> >
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Daniel Brewer ★ 1.9k
@daniel-brewer-1791
Last seen 10.3 years ago
Yes I have already tried that, class(expression) is matrix. But class(expression[1,]) is list as is class(expression[,1]). Whereas the class of my simple constructed matrix when looking at a single row or column is numeric i.e. class(togo[,2]). Thanks for the suggestion anyway. Stephen Henderson wrote: > Are you sure expression is a matrix? > What do you get when you type? > >> class(expression) > > have you tried: > >> expression<- as.matrix(expression) > > > Stephen Henderson > Wolfson Inst. for Biomedical Research > Cruciform Bldg., Gower Street > University College London > United Kingdom, WC1E 6BT > +44 (0)207 679 6827 > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Daniel > Brewer > Sent: 30 March 2007 14:42 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] matrix row/column displayed as a list > > Hi, > > This is a silly little question, but I can't find the answer. I have a > matrix of expression values e.g. expression. When I display either one > column or one row it displays a list e.g. expression[1,] or > expression[,1]. Is there a way to change this behaviour? > > When I constructed a test matrix, the matrix worked as desired i.e. >> togo <- matrix(c(1,2,3,4),ncol=2, nrow=2) >> togo[,1] > [1] 1 2 > Why is the behaviour different? > > Many thanks > > Dan The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addre...{{dropped}}
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