Hi everyone, I would like to thank Zhao, Xiaohong (NIH/NCI) [zhaoxiao@mail.nih.gov] Tarca Adi Laurentiu [ltarca@rsvs.ulaval.ca] James MacDonald" <jmacdon@med.umich.edu> who gave me valuable suggestions. Based on these I did the following and it worked: > source("http://www.bioconductor.org/getBioC.R") > getBioC(develOK=TRUE) > install.packages2("affy",develOK=T) Melania Rm 15-433, ext 4886 Fax: (416) 946-2048 -----Original Message----- From: bioconductor-request@stat.math.ethz.ch [mailto:bioconductor-request@stat.math.ethz.ch] Sent: Thursday, October 28, 2004 6:07 AM To: bioconductor@stat.math.ethz.ch Subject: Bioconductor Digest, Vol 20, Issue 27 Send Bioconductor mailing list submissions to bioconductor@stat.math.ethz.ch To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/listinfo/bioconductor or, via email, send a message with subject or body 'help' to bioconductor-request@stat.math.ethz.ch You can reach the person managing the list at bioconductor-owner@stat.math.ethz.ch When replying, please edit your Subject line so it is more specific than "Re: Contents of Bioconductor digest..." Today's Topics: 1. GeneExpressionOmnibus (GEO) question (Ilya Venger) 2. normalization with large amount of significant genes (Ana Conesa) 3. Combining MOE430A and MOE4302 (Scott Ochsner) 4. error readAffy (Auer Michael) 5. Loading package multtest (Prof. Dr. L. Hothorn) 6. reposTools: problem with download.packages2 (Matthias Burger) 7. Re: reposTools: problem with download.packages2 (Jeff Gentry) 8. How can I put color scale & legend on Heatmap (Saurin Jani) 9. Re: Combining MOE430A and MOE4302 (Wolfgang Huber) 10. Problem installing graph package (Matt McCall) 11. Re: Problem installing graph package (Robert Gentleman) 12. globaltest : geneplot & sample plot (Saurin Jani) 13. Missing GO terms in GOLOCUSID2GO (jeffrey rasmussen) 14. Re: Missing GO terms in GOLOCUSID2GO (Robert Gentleman) 15. Re: Problem installing graph package (Byron Ellis) 16. Re: Color in the lefs of a dendrogram? (Martin Maechler) 17. Comparison of Affymetrix and CodeLink chip (Binita Dutta) ---------------------------------------------------------------------- Message: 1 Date: Wed, 27 Oct 2004 13:33:36 +0200 From: Ilya Venger <ilya.venger@weizmann.ac.il> Subject: [BioC] GeneExpressionOmnibus (GEO) question To: bioconductor@stat.math.ethz.ch Message-ID: <417F8790.3040100@weizmann.ac.il> Content-Type: text/plain; charset=us-ascii; format=flowed I know that I can query the GEO database using the AnnBuilder package. However, I don't know exactly what to do next. NCBI states that the data they present in GDS accessions is normalized, but they don't explain how. The GSMs of different contributors not necessarily match, and they sometimes lack parts of the data. Also, if the raw data is submitted, how come they don't show the measurements for both repetitions of each gene in a cDNA array. Another problem, is that although the GDS are claimed to be normalized the sum of logs for all genes on a chip doesn't sum to 0. So, if anybody worked with GEO before, and has experience at it I would be glad to pose several more specific questions. ------------------------------ Message: 2 Date: Wed, 27 Oct 2004 15:47:53 +0200 From: Ana Conesa <aconesa@ivia.es> Subject: [BioC] normalization with large amount of significant genes To: bioconductor@stat.math.ethz.ch Message-ID: <6.1.0.6.0.20041027132513.01c5ee00@master.ivia.es> Content-Type: text/plain; charset="iso-8859-1" ------------------------------ Message: 3 Date: Wed, 27 Oct 2004 09:15:59 -0500 From: "Scott Ochsner" <sochsner@bcm.tmc.edu> Subject: [BioC] Combining MOE430A and MOE4302 To: "'Bioconductor'" <bioconductor@stat.math.ethz.ch> Message-ID: <200410271416.JAA15363@bran.bcm.tmc.edu> Content-Type: text/plain I have two sets of CEL files: one from MOE430A and one from MOE4302. I would like to normalize similar probe sets across the chip types but I am unable to combine Affybatches as they are different sizes. This was touched on previously in this list serve concerning the combination of HGU133A and HGU133 Plus2.0 chips. I could not, however, find an answer to the problem in this thread. I was thinking I could restructure the existing MOE4302 affybatch by subtracting/removing the MOE430B probe set data and then proceed to combining this with the existing MOE430A affybatch. I am able to perform routine R manipulations but the subtracting scheme detailed above is beyond my scope. Scott Ochsner, Ph.D. Huffington Center on Aging, M810 Baylor College of Medicine Houston, TX. 77030 Lab: 713-798-1620 Office: 713-798-1585 [[alternative HTML version deleted]] ------------------------------ Message: 4 Date: Wed, 27 Oct 2004 16:23:25 +0200 (CEST) From: "Auer Michael" <michael.auer@meduniwien.ac.at> Subject: [BioC] error readAffy To: bioconductor@stat.math.ethz.ch Message-ID: <1284.80.108.125.179.1098887005.squirrel@80.108.125.179> Content-Type: text/plain;charset=iso-8859-1 I am using Windows XP, R 2.0.0. and affy package 1.5.8 I have copied the files to the folder "//Marvel- xms4rmgc/festplatte/A2M Lab/01 Customers/AKH/Erowic/data/filename.cel" sample.names<- c("SCC9_A_0"," SCC9_A_C"," SCC9_A_N"," SCC9_A_CN", "SCC9_B_0"," SCC9_B_C"," SCC9_B_N"," SCC9_B_CN", "SCC9_C_0"," SCC9_C_C"," SCC9_C_N"," SCC9_C_CN") sample.files<-c("//Marvel-xms4rmgc/festplatte/A2M Lab/01 Customers/AKH/Erowic/data/BE_102104_sampleSSC 9 A o.CEL", "//Marvel-xms4rmgc/festplatte/A2M Lab/01 Customers/AKH/Erowic/data/BE_102104_sampleSSC 9 A c.CEL", "//Marvel-xms4rmgc/festplatte/A2M Lab/01 Customers/AKH/Erowic/data/BE_102104_sampleSSC9 A n.CEL", "//Marvel-xms4rmgc/festplatte/A2M Lab/01 Customers/AKH/Erowic/data/BE_102104_sampleSSC 9 A c+n.CEL", "//Marvel-xms4rmgc/festplatte/A2M Lab/01 Customers/AKH/Erowic/data/BE_102104_sampleSSC 9 B o.CEL", "//Marvel-xms4rmgc/festplatte/A2M Lab/01 Customers/AKH/Erowic/data/BE_102104_sampleSSC 9 B c.CEL", "//Marvel-xms4rmgc/festplatte/A2M Lab/01 Customers/AKH/Erowic/data/BE_102104_sampleSSC 9 B n.CEL", "//Marvel-xms4rmgc/festplatte/A2M Lab/01 Customers/AKH/Erowic/data/BE_102104_sampleSSC 9 B c+n.CEL", "//Marvel-xms4rmgc/festplatte/A2M Lab/01 Customers/AKH/Erowic/data/BE_102204_sample SSC9 C o.CEL", "//Marvel-xms4rmgc/festplatte/A2M Lab/01 Customers/AKH/Erowic/data/BE_102204_sample SSC9 C c.CEL", "//Marvel-xms4rmgc/festplatte/A2M Lab/01 Customers/AKH/Erowic/data/BE_102204_sample SSC9 C n.CEL", "//Marvel-xms4rmgc/festplatte/A2M Lab/01 Customers/AKH/Erowic/data/BE_102204_sample SSC9 C c+n.CEL") I am loading the library library(affy) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: reposTools Then I am using ReadAffy and the following error message occurs with two of the arrays. pleca<-ReadAffy(filenames=sample.files,sampleNames =sample.names) Error in initialize(value, ...) : Could not open file //Marvel-xm 4rmgc/festplatte/A2M Lab/01 Customers/AKH/Erowic/data/BE_102204_sample SSC9 C n.CEL What is the problem? Can anybody help. I can't go back to a former release, because R 2.0.0. doesn't accept it. Thanks ------------------------------ Message: 5 Date: Wed, 27 Oct 2004 08:58:57 +0200 From: "Prof. Dr. L. Hothorn" <hothorn@bioinf.uni-hannover.de> Subject: [BioC] Loading package multtest To: bioconductor@stat.math.ethz.ch Message-ID: <6.0.0.22.0.20041027085714.01c15e60@mail.bioinf.uni- hannover.de> Content-Type: text/plain; charset="us-ascii" ------------------------------ Message: 6 Date: Wed, 27 Oct 2004 12:24:52 +0200 From: Matthias Burger <matthias.burger@epigenomics.com> Subject: [BioC] reposTools: problem with download.packages2 To: bioconductor@stat.math.ethz.ch Message-ID: <417F7774.3090404@epigenomics.com> Content-Type: text/plain; charset=us-ascii; format=flowed Hi, i used the following calls to download all of Windows packages stored on the BioC CRAN mirror, but the executions tops with an error report on a package (CoCo) only available as source pkg. Did I make a mistake, or misunderstand the docu? I had thought the type argument would take care of this? Thanks for any adivse how to get this working. Regards, Matthias z <- repositories() ## select: 1 ok <- download.packages2(repEntry=z, destDir="/mnt/local/R/windows/R-contrib/contrib-2.0.0/CRAN/", type="Win32") ... [1] "Attempting to download CoCoAn from http://www.bioconductor.org//CRANrepository" [1] "Download complete." Error in download.packages2(repEntry = z, destDir = "/mnt/local/R/windows/R-contrib/contrib-2.0.0/CRAN/", : Package CoCo is not available at http://www.bioconductor.org//CRANrepository details: reposTools 1.4.13 >version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 0.0 year 2004 month 10 day 04 language R -- Matthias Burger Project Manager/ Biostatistician Epigenomics AG Kleine Praesidentenstr. 1 10178 Berlin, Germany phone:+49-30-24345-371 fax:+49-30-24345-555 http://www.epigenomics.com matthias.burger@epigenomics.com ------------------------------ Message: 7 Date: Wed, 27 Oct 2004 10:35:40 -0400 (EDT) From: Jeff Gentry <jgentry@jimmy.harvard.edu> Subject: Re: [BioC] reposTools: problem with download.packages2 To: Matthias Burger <matthias.burger@epigenomics.com> Cc: bioconductor@stat.math.ethz.ch Message-ID: <pine.sol.4.20.0410271035000.18197-100000@santiam.dfci.harvard.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII > i used the following calls to download all of Windows packages stored > on the BioC CRAN mirror, but the executions tops with an error report on > a package (CoCo) only available as source pkg. Well, it is only avail as a source package. :) Did the execution halt right there, or did it get all of the packages and just say that it couldn't get CoCo at the end? Not sure exactly which you're describing here. ------------------------------ Message: 8 Date: Wed, 27 Oct 2004 08:42:10 -0700 (PDT) From: Saurin Jani <saurin_jani@yahoo.com> Subject: [BioC] How can I put color scale & legend on Heatmap To: Bioconductor Bioconductor <bioconductor@stat.math.ethz.ch> Message-ID: <20041027154210.65125.qmail@web41124.mail.yahoo.com> Content-Type: text/plain; charset=us-ascii Hi, On my heatmap, I am doing: > rbg <- maPalette(low="blue", high="red", mid="white") > Feature_GeneNames <- mget(unique(myFeatureGenes),env = moe430aGENENAME); > row.names(esetFeatureX) <- Feature_GeneNames; > colnames(esetFeatureX) <- samples; > heatmap(esetFeatureX,Rowv= NA ,Colv= NA,col=rbg,margins=c(10,30)); I can see nice heat map, but how should I put legend on heatmap image because legend() does seem to work in combination of heatmap. May be I am doing something wrong. How can I put legend & color scale below heatmap image. Any heatmap suggestion would be great..! Thank you, Saurin ------------------------------ Message: 9 Date: Wed, 27 Oct 2004 19:47:40 +0100 From: Wolfgang Huber <huber@ebi.ac.uk> Subject: Re: [BioC] Combining MOE430A and MOE4302 To: bioconductor@stat.math.ethz.ch Message-ID: <417FED4C.9080302@ebi.ac.uk> Content-Type: text/plain; charset=us-ascii; format=flowed Scott Ochsner wrote: > I have two sets of CEL files: one from MOE430A and one from MOE4302. I > would like to normalize similar probe sets across the chip types but I am > unable to combine Affybatches as they are different sizes. This was touched > on previously in this list serve concerning the combination of HGU133A and > HGU133 Plus2.0 chips. I could not, however, find an answer to the problem > in this thread. Can you be more be more specific about "unable to combine Affybatches as they are different sizes"? Did you try the function combineAffyBatcg from package matchprobes? Bw Wolfgang -- ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Http: www.dkfz.de/abt0840/whuber ------------------------------ Message: 10 Date: Wed, 27 Oct 2004 14:28:50 -0400 From: Matt McCall <mmccall@mail.nih.gov> Subject: [BioC] Problem installing graph package To: bioconductor@stat.math.ethz.ch Message-ID: <0CB2F3EB-2846-11D9-B275-000A95AFE190@mail.nih.gov> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Using R v2.0.0 on MacOS X in the R console. I was able to install most of bioconductor. I wanted to use the GOstats package (amoung a few others), and it didn't install properly. So I went back to try to find the problem, and it seems that the graph package isn't installing. Any suggestions? Matt > getBioC("prog", develOK=T) Running getBioC version 1.2.66.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. Please select an installation directory: 1:/Users/mmccall/Library/R/library 2:/Library/Frameworks/R.framework/Resources/library Selection: 1 [1] "Attempting to download graph from http://www.bioconductor.org/repository/devel/package/Source" [1] "Download complete." [1] "Installing graph" * Installing *source* package 'graph' ... ** libs gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c graph.c -o graph.o graph.c: In function `intersectStrings': graph.c:39: warning: assignment makes pointer from integer without a cast graph.c:56: warning: assignment makes pointer from integer without a cast graph.c: In function `graphIntersection': graph.c:118: warning: assignment makes pointer from integer without a cast graph.c: In function `checkEdgeList': graph.c:157: warning: assignment makes pointer from integer without a cast gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o graph.so graph.o -lcc_dynamic -framework R ld: warning multiple definitions of symbol _xerbla_ /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_ /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of _xerbla_ ld: warning multiple definitions of symbol _crc32 /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32 /usr/lib/libz.1.dylib(crc32.o) definition of _crc32 ld: warning multiple definitions of symbol _get_crc_table /Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table ld: warning multiple definitions of symbol _deflate /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate /usr/lib/libz.1.dylib(deflate.o) definition of _deflate ld: warning multiple definitions of symbol _deflateCopy /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy ld: warning multiple definitions of symbol _deflateReset /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateReset /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset ld: warning multiple definitions of symbol _deflateSetDictionary /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateSetDictionary /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary ld: warning multiple definitions of symbol _deflateInit2_ /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateInit2_ /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_ ld: warning multiple definitions of symbol _deflateEnd /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd ld: warning multiple definitions of symbol _deflateParams /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateParams /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams ld: warning multiple definitions of symbol _deflateInit_ /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateInit_ /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_ ld: warning multiple definitions of symbol _zError /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError /usr/lib/libz.1.dylib(zutil.o) definition of _zError ld: warning multiple definitions of symbol _zlibVersion /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion ld: warning multiple definitions of symbol _inflateEnd /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd ld: warning multiple definitions of symbol _inflateSync /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync ld: warning multiple definitions of symbol _inflateSyncPoint /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSyncPoint /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint ld: warning multiple definitions of symbol _inflate /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate /usr/lib/libz.1.dylib(inflate.o) definition of _inflate ld: warning multiple definitions of symbol _inflateSetDictionary /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSetDictionary /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary ld: warning multiple definitions of symbol _inflateInit2_ /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateInit2_ /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_ ld: warning multiple definitions of symbol _inflateReset /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateReset /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset ld: warning multiple definitions of symbol _inflateInit_ /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateInit_ /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_ ld: warning multiple definitions of symbol _adler32 /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32 /usr/lib/libz.1.dylib(adler32.o) definition of _adler32 ld: warning multiple definitions of symbol _BC /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ libreadline.4.3.dylibterminal.so) definition of _BC /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC ld: warning multiple definitions of symbol _UP /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ libreadline.4.3.dylibterminal.so) definition of _UP /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP ld: warning multiple definitions of symbol _PC /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ libreadline.4.3.dylibterminal.so) definition of _PC /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC ld: warning multiple definitions of symbol _gzeof /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof /usr/lib/libz.1.dylib(gzio.o) definition of _gzeof ld: warning multiple definitions of symbol _gzclose /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose /usr/lib/libz.1.dylib(gzio.o) definition of _gzclose ld: warning multiple definitions of symbol _gzdopen /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen /usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen ld: warning multiple definitions of symbol _gzerror /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror /usr/lib/libz.1.dylib(gzio.o) definition of _gzerror ld: warning multiple definitions of symbol _gzflush /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush /usr/lib/libz.1.dylib(gzio.o) definition of _gzflush ld: warning multiple definitions of symbol _gzgetc /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc /usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc ld: warning multiple definitions of symbol _gzgets /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets /usr/lib/libz.1.dylib(gzio.o) definition of _gzgets ld: warning multiple definitions of symbol _gzopen /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen /usr/lib/libz.1.dylib(gzio.o) definition of _gzopen ld: warning multiple definitions of symbol _gzprintf /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf /usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf ld: warning multiple definitions of symbol _gzputc /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc /usr/lib/libz.1.dylib(gzio.o) definition of _gzputc ld: warning multiple definitions of symbol _gzputs /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs /usr/lib/libz.1.dylib(gzio.o) definition of _gzputs ld: warning multiple definitions of symbol _gzread /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread /usr/lib/libz.1.dylib(gzio.o) definition of _gzread ld: warning multiple definitions of symbol _gzrewind /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind /usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind ld: warning multiple definitions of symbol _gzseek /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek /usr/lib/libz.1.dylib(gzio.o) definition of _gzseek ld: warning multiple definitions of symbol _gzsetparams /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams /usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams ld: warning multiple definitions of symbol _gztell /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell /usr/lib/libz.1.dylib(gzio.o) definition of _gztell ld: warning multiple definitions of symbol _gzwrite /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite /usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite ** R ** data ** inst ** save image [1] TRUE [1] TRUE [1] TRUE Loading required package: cluster Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. [1] "propertyHolder" [1] "property" [1] "property" [1] "property<-" [1] "property<-" [1] "asGraphProperty" [1] "asGraphProperty" [1] "asGraphProperty" [1] "asGraphProperty" [1] "asGraphProperty" [1] "graph" [1] "edgemode" [1] "edgemode" [1] "edgemode<-" [1] "edgemode<-" [1] "graphNEL" [1] "initialize" [1] "nodes" [1] "nodes" [1] "nodes<-" [1] "nodes<-" [1] "edges" [1] "edges" [1] "edges" [1] "degree" [1] "degree" [1] "degree" [1] "edgeWeights" [1] "edgeWeights" [1] "adj" [1] "adj" [1] "acc" [1] "acc" [1] "DFS" [1] "DFS" [1] "edgeL" [1] "edgeL" [1] "subGraph" [1] "subGraph" [1] "intersection2" [1] "intersection2" [1] "intersection" [1] "intersection" [1] "join" [1] "join" [1] "union" [1] "union" [1] "complement" [1] "complement" [1] "connComp" [1] "connComp" [1] "isConnected" [1] "isConnected" [1] "numNodes" [1] "numNodes" [1] "numNodes" [1] "addNode" [1] "addNode" [1] "addNode" [1] "removeNode" [1] "removeNode" [1] "clearNode" [1] "clearNode" [1] "removeEdge" [1] "removeEdge" [1] "addEdge" [1] "addEdge" [1] "combineNodes" [1] "combineNodes" [1] "inEdges" [1] "inEdges" [1] "inEdges" [1] "inEdges" [1] "show" [1] "edgeNames" [1] "edgeNames" [1] "clusteringCoefficient" [1] "clusteringCoefficient" Error in assign("nullgraphID", getuuid()) : couldn't find function "getuuid" Execution halted cat: ** Removing '/Users/mmccall/Library/R/library/graph' ** Restoring previous '/Users/mmccall/Library/R/library/graph' stdout: Broken pipe ERROR: execution of package source for 'graph' failed [1] "Attempting to download hexbin from http://www.bioconductor.org/repository/devel/package/Source" [1] "Download complete." [1] "Installing hexbin" * Installing *source* package 'hexbin' ... ** libs g77 -fno-common -g -O2 -c hbin.f -o hbin.o ** Removing '/Users/mmccall/Library/R/library/hexbin' make: g77: Command not found make: *** [hbin.o] Error 127 ERROR: compilation failed for package 'hexbin' ** Restoring previous '/Users/mmccall/Library/R/library/hexbin' [1] "Attempting to download Ruuid from http://www.bioconductor.org/repository/devel/package/Source" [1] "Download complete." [1] "Installing Ruuid" * Installing *source* package 'Ruuid' ... creating cache ./config.cache checking for glib-config... no checking how to run the C preprocessor... cc -E checking for /usr/include/unistd.h... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include/glib12 -DHAVE_UNISTD_H=1 -I/usr/local/include -fno-common -g -O2 -c Rinit.c -o Rinit.o In file included from Ruuid.h:5, from Rinit.c:1: uuidP.h:24:18: glib.h: No such file or directory In file included from Ruuid.h:5, from Rinit.c:1: uuidP.h:36: error: parse error before "guint32" uuidP.h:36: warning: no semicolon at end of struct or union uuidP.h:37: warning: data definition has no type or storage class uuidP.h:38: error: parse error before "time_hi_and_version" uuidP.h:38: warning: data definition has no type or storage class uuidP.h:39: error: parse error before "clock_seq" uuidP.h:39: warning: data definition has no type or storage class uuidP.h:40: error: parse error before "node" uuidP.h:40: warning: data definition has no type or storage class uuidP.h:41: error: parse error before '}' token ** Removing '/Users/mmccall/Library/R/library/Ruuid' ** Restoring previous '/Users/mmccall/Library/R/library/Ruuid' make: *** [Rinit.o] Error 1 ERROR: compilation failed for package 'Ruuid' From URL: http://www.bioconductor.org/repository/devel/package/Source graph version 1.4.22 hexbin version 1.1-2 Ruuid version 1.4.5 Packages Rgraphviz and rhdf5 require special libraries to be installed. Please see the URL http://www.bioconductor.org/faq.html#Other Notes for more details on installing these packages if they fail to install properly Warning messages: 1: Installation of package graph had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 2: Installation of package hexbin had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 3: Installation of package Ruuid had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > ------------------------------ Message: 11 Date: Wed, 27 Oct 2004 14:44:41 -0400 From: Robert Gentleman <rgentlem@jimmy.harvard.edu> Subject: Re: [BioC] Problem installing graph package To: Matt McCall <mmccall@mail.nih.gov> Cc: bioconductor@stat.math.ethz.ch Message-ID: <20041027144441.A5500@jimmy.harvard.edu> Content-Type: text/plain; charset=us-ascii Hi, First your real problem is that you do not have Ruuid installed (and that is what graph reports as the problem). So that would be your first port of call. There are some details of how to do this, and what libraries you need in the mailing list archives. so do install.packages2("Ruuid") and then see what libraries you do not have installed on your system, then get them and install them. Second, you do not have g77, so you won't be able to install any fortran code (and that is what is in hexbin). Again, this is because you lack the right tools in OS X, so you need to find them and install them. Stefano Iacus keeps a nice web page that describes what you need to have installed etc. for building R packages. The OS X FAQ, is another place to look for details (and probably the first place to look), Best Robert On Wed, Oct 27, 2004 at 02:28:50PM -0400, Matt McCall wrote: > Using R v2.0.0 on MacOS X in the R console. > I was able to install most of bioconductor. I wanted to use the GOstats > package (amoung a few others), and it didn't install properly. So I > went back to try to find the problem, and it seems that the graph > package isn't installing. Any suggestions? > Matt > > > getBioC("prog", develOK=T) > Running getBioC version 1.2.66.... > If you encounter problems, first make sure that > you are running the latest version of getBioC() > which can be found at: www.bioconductor.org/getBioC.R > > Please direct any concerns or questions to > bioconductor@stat.math.ethz.ch. > > Please select an installation directory: > 1:/Users/mmccall/Library/R/library > 2:/Library/Frameworks/R.framework/Resources/library > Selection: 1 > [1] "Attempting to download graph from > http://www.bioconductor.org/repository/devel/package/Source" > [1] "Download complete." > [1] "Installing graph" > * Installing *source* package 'graph' ... > ** libs > gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include > -I/usr/local/include -fno-common -g -O2 -c graph.c -o graph.o > graph.c: In function `intersectStrings': > graph.c:39: warning: assignment makes pointer from integer without a > cast > graph.c:56: warning: assignment makes pointer from integer without a > cast > graph.c: In function `graphIntersection': > graph.c:118: warning: assignment makes pointer from integer without a > cast > graph.c: In function `checkEdgeList': > graph.c:157: warning: assignment makes pointer from integer without a > cast > gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o > graph.so graph.o -lcc_dynamic -framework R > ld: warning multiple definitions of symbol _xerbla_ > /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_ > /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ > vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of > _xerbla_ > ld: warning multiple definitions of symbol _crc32 > /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32 > /usr/lib/libz.1.dylib(crc32.o) definition of _crc32 > ld: warning multiple definitions of symbol _get_crc_table > /Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table > /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table > ld: warning multiple definitions of symbol _deflate > /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate > /usr/lib/libz.1.dylib(deflate.o) definition of _deflate > ld: warning multiple definitions of symbol _deflateCopy > /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy > /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy > ld: warning multiple definitions of symbol _deflateReset > /Library/Frameworks/R.framework/R(deflate.lo) definition of > _deflateReset > /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset > ld: warning multiple definitions of symbol _deflateSetDictionary > /Library/Frameworks/R.framework/R(deflate.lo) definition of > _deflateSetDictionary > /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary > ld: warning multiple definitions of symbol _deflateInit2_ > /Library/Frameworks/R.framework/R(deflate.lo) definition of > _deflateInit2_ > /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_ > ld: warning multiple definitions of symbol _deflateEnd > /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd > /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd > ld: warning multiple definitions of symbol _deflateParams > /Library/Frameworks/R.framework/R(deflate.lo) definition of > _deflateParams > /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams > ld: warning multiple definitions of symbol _deflateInit_ > /Library/Frameworks/R.framework/R(deflate.lo) definition of > _deflateInit_ > /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_ > ld: warning multiple definitions of symbol _zError > /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError > /usr/lib/libz.1.dylib(zutil.o) definition of _zError > ld: warning multiple definitions of symbol _zlibVersion > /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion > /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion > ld: warning multiple definitions of symbol _inflateEnd > /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd > /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd > ld: warning multiple definitions of symbol _inflateSync > /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync > /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync > ld: warning multiple definitions of symbol _inflateSyncPoint > /Library/Frameworks/R.framework/R(inflate.lo) definition of > _inflateSyncPoint > /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint > ld: warning multiple definitions of symbol _inflate > /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate > /usr/lib/libz.1.dylib(inflate.o) definition of _inflate > ld: warning multiple definitions of symbol _inflateSetDictionary > /Library/Frameworks/R.framework/R(inflate.lo) definition of > _inflateSetDictionary > /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary > ld: warning multiple definitions of symbol _inflateInit2_ > /Library/Frameworks/R.framework/R(inflate.lo) definition of > _inflateInit2_ > /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_ > ld: warning multiple definitions of symbol _inflateReset > /Library/Frameworks/R.framework/R(inflate.lo) definition of > _inflateReset > /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset > ld: warning multiple definitions of symbol _inflateInit_ > /Library/Frameworks/R.framework/R(inflate.lo) definition of > _inflateInit_ > /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_ > ld: warning multiple definitions of symbol _adler32 > /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32 > /usr/lib/libz.1.dylib(adler32.o) definition of _adler32 > ld: warning multiple definitions of symbol _BC > /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ > libreadline.4.3.dylibterminal.so) definition of _BC > /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC > ld: warning multiple definitions of symbol _UP > /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ > libreadline.4.3.dylibterminal.so) definition of _UP > /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP > ld: warning multiple definitions of symbol _PC > /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ > libreadline.4.3.dylibterminal.so) definition of _PC > /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC > ld: warning multiple definitions of symbol _gzeof > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof > /usr/lib/libz.1.dylib(gzio.o) definition of _gzeof > ld: warning multiple definitions of symbol _gzclose > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose > /usr/lib/libz.1.dylib(gzio.o) definition of _gzclose > ld: warning multiple definitions of symbol _gzdopen > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen > /usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen > ld: warning multiple definitions of symbol _gzerror > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror > /usr/lib/libz.1.dylib(gzio.o) definition of _gzerror > ld: warning multiple definitions of symbol _gzflush > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush > /usr/lib/libz.1.dylib(gzio.o) definition of _gzflush > ld: warning multiple definitions of symbol _gzgetc > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc > /usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc > ld: warning multiple definitions of symbol _gzgets > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets > /usr/lib/libz.1.dylib(gzio.o) definition of _gzgets > ld: warning multiple definitions of symbol _gzopen > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen > /usr/lib/libz.1.dylib(gzio.o) definition of _gzopen > ld: warning multiple definitions of symbol _gzprintf > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf > /usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf > ld: warning multiple definitions of symbol _gzputc > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc > /usr/lib/libz.1.dylib(gzio.o) definition of _gzputc > ld: warning multiple definitions of symbol _gzputs > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs > /usr/lib/libz.1.dylib(gzio.o) definition of _gzputs > ld: warning multiple definitions of symbol _gzread > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread > /usr/lib/libz.1.dylib(gzio.o) definition of _gzread > ld: warning multiple definitions of symbol _gzrewind > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind > /usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind > ld: warning multiple definitions of symbol _gzseek > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek > /usr/lib/libz.1.dylib(gzio.o) definition of _gzseek > ld: warning multiple definitions of symbol _gzsetparams > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams > /usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams > ld: warning multiple definitions of symbol _gztell > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell > /usr/lib/libz.1.dylib(gzio.o) definition of _gztell > ld: warning multiple definitions of symbol _gzwrite > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite > /usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite > ** R > ** data > ** inst > ** save image > [1] TRUE > [1] TRUE > [1] TRUE > Loading required package: cluster > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > [1] "propertyHolder" > [1] "property" > [1] "property" > [1] "property<-" > [1] "property<-" > [1] "asGraphProperty" > [1] "asGraphProperty" > [1] "asGraphProperty" > [1] "asGraphProperty" > [1] "asGraphProperty" > [1] "graph" > [1] "edgemode" > [1] "edgemode" > [1] "edgemode<-" > [1] "edgemode<-" > [1] "graphNEL" > [1] "initialize" > [1] "nodes" > [1] "nodes" > [1] "nodes<-" > [1] "nodes<-" > [1] "edges" > [1] "edges" > [1] "edges" > [1] "degree" > [1] "degree" > [1] "degree" > [1] "edgeWeights" > [1] "edgeWeights" > [1] "adj" > [1] "adj" > [1] "acc" > [1] "acc" > [1] "DFS" > [1] "DFS" > [1] "edgeL" > [1] "edgeL" > [1] "subGraph" > [1] "subGraph" > [1] "intersection2" > [1] "intersection2" > [1] "intersection" > [1] "intersection" > [1] "join" > [1] "join" > [1] "union" > [1] "union" > [1] "complement" > [1] "complement" > [1] "connComp" > [1] "connComp" > [1] "isConnected" > [1] "isConnected" > [1] "numNodes" > [1] "numNodes" > [1] "numNodes" > [1] "addNode" > [1] "addNode" > [1] "addNode" > [1] "removeNode" > [1] "removeNode" > [1] "clearNode" > [1] "clearNode" > [1] "removeEdge" > [1] "removeEdge" > [1] "addEdge" > [1] "addEdge" > [1] "combineNodes" > [1] "combineNodes" > [1] "inEdges" > [1] "inEdges" > [1] "inEdges" > [1] "inEdges" > [1] "show" > [1] "edgeNames" > [1] "edgeNames" > [1] "clusteringCoefficient" > [1] "clusteringCoefficient" > Error in assign("nullgraphID", getuuid()) : > couldn't find function "getuuid" > Execution halted > cat: ** Removing '/Users/mmccall/Library/R/library/graph' > ** Restoring previous '/Users/mmccall/Library/R/library/graph' > stdout: Broken pipe > ERROR: execution of package source for 'graph' failed > [1] "Attempting to download hexbin from > http://www.bioconductor.org/repository/devel/package/Source" > [1] "Download complete." > [1] "Installing hexbin" > * Installing *source* package 'hexbin' ... > ** libs > g77 -fno-common -g -O2 -c hbin.f -o hbin.o > ** Removing '/Users/mmccall/Library/R/library/hexbin' > make: g77: Command not found > make: *** [hbin.o] Error 127 > ERROR: compilation failed for package 'hexbin' > ** Restoring previous '/Users/mmccall/Library/R/library/hexbin' > [1] "Attempting to download Ruuid from > http://www.bioconductor.org/repository/devel/package/Source" > [1] "Download complete." > [1] "Installing Ruuid" > * Installing *source* package 'Ruuid' ... > creating cache ./config.cache > checking for glib-config... no > checking how to run the C preprocessor... cc -E > checking for /usr/include/unistd.h... yes > updating cache ./config.cache > creating ./config.status > creating src/Makevars > ** libs > gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include > -I/usr/local/include/glib12 -DHAVE_UNISTD_H=1 -I/usr/local/include > -fno-common -g -O2 -c Rinit.c -o Rinit.o > In file included from Ruuid.h:5, > from Rinit.c:1: > uuidP.h:24:18: glib.h: No such file or directory > In file included from Ruuid.h:5, > from Rinit.c:1: > uuidP.h:36: error: parse error before "guint32" > uuidP.h:36: warning: no semicolon at end of struct or union > uuidP.h:37: warning: data definition has no type or storage class > uuidP.h:38: error: parse error before "time_hi_and_version" > uuidP.h:38: warning: data definition has no type or storage class > uuidP.h:39: error: parse error before "clock_seq" > uuidP.h:39: warning: data definition has no type or storage class > uuidP.h:40: error: parse error before "node" > uuidP.h:40: warning: data definition has no type or storage class > uuidP.h:41: error: parse error before '}' token > ** Removing '/Users/mmccall/Library/R/library/Ruuid' > ** Restoring previous '/Users/mmccall/Library/R/library/Ruuid' > make: *** [Rinit.o] Error 1 > ERROR: compilation failed for package 'Ruuid' > From URL: http://www.bioconductor.org/repository/devel/package/Source > graph version 1.4.22 > hexbin version 1.1-2 > Ruuid version 1.4.5 > > Packages Rgraphviz and rhdf5 require special libraries to be installed. > Please see the URL http://www.bioconductor.org/faq.html#Other Notes for > more details on installing these packages if they fail > to install properly > > Warning messages: > 1: Installation of package graph had non-zero exit status in: > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > 2: Installation of package hexbin had non-zero exit status in: > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > 3: Installation of package Ruuid had non-zero exit status in: > installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------ + | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------ + ------------------------------ Message: 12 Date: Wed, 27 Oct 2004 12:22:22 -0700 (PDT) From: Saurin Jani <saurin_jani@yahoo.com> Subject: [BioC] globaltest : geneplot & sample plot To: Bioconductor Bioconductor <bioconductor@stat.math.ethz.ch> Message-ID: <20041027192222.38645.qmail@web41112.mail.yahoo.com> Content-Type: text/plain; charset=us-ascii Hi, > path1 <- kegg[["00280"]]; > globaltest_all <- globaltest(esetSub2,pData(esetSub2)[,"scanner2"],test.genes = path1,model = "logistic"); > geneplot(globaltest_all,labelsize = 1); here, it shows only 1 gene(145512_at) out of my all 6 samples. I have 3 Knock Out and 3 Wild Type samples. > sampleplot(globaltest_all,labelsize = 1); here, I can see all 6 sample plots look similar , Knock out and Wild Type. Very less difference. I think , it should only show Knock out sample at higher bar..right..! Am I doing something wrong or I have wrong undertanding..about sampleplot and geneplots. (or Need to read more about that) Please let me know..if anyone..! Thanks, Saurin ------------------------------ Message: 13 Date: Wed, 27 Oct 2004 13:36:18 -0700 (PDT) From: jeffrey rasmussen <rasmuss@u.washington.edu> Subject: [BioC] Missing GO terms in GOLOCUSID2GO To: bioconductor@stat.math.ethz.ch Message-ID: <pine.a41.4.61b.0410271322460.264822@homer11.u.washington.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Using GO 1.6.5 the following code produces a list of GO terms that are annotated as being connected with a certain LL id, but have their "Ontology" slot listed as "NA" (presumably because they are missing from GOTERM and the other GO* objects): library(GO) ll2go <- as.list.environment(GOLOCUSID2GO) tmp <- lapply(ll2go, function (x) sapply(x, function(x) ifis.na(x$Ontology)){ print(x$GOID) })) Perhaps a more recent file was used to build GOLOCUSID2GO than was used to build the remaining GO annotations? Jeff. (Here's the list of missing terms) GO:0001880 GO:0001881 GO:0001883 GO:0001886 GO:0030968 GO:0030970 GO:0030971 GO:0035199 GO:0035211 GO:0035214 GO:0035215 GO:0035224 GO:0035226 GO:0035227 GO:0035229 GO:0035232 GO:0035233 GO:0035234 GO:0043185 GO:0043190 GO:0043197 GO:0043198 GO:0048488 GO:0048489 GO:0051082 GO:0051087 GO:0051089 GO:0051092 GO:0051097 GO:0051101 GO:0051106 ------------------------------ Message: 14 Date: Wed, 27 Oct 2004 16:41:49 -0400 From: Robert Gentleman <rgentlem@jimmy.harvard.edu> Subject: Re: [BioC] Missing GO terms in GOLOCUSID2GO To: jeffrey rasmussen <rasmuss@u.washington.edu> Cc: bioconductor@stat.math.ethz.ch Message-ID: <20041027164149.H5500@jimmy.harvard.edu> Content-Type: text/plain; charset=us-ascii Funny you should ask... yes we just noticed this. It seems to be a problem somewhere in the data we obtained. It is most likely that we will drop these - they can often be hand curated, but hands are the one thing we are very short of...so anyone looking for something constructive to do...we have lots of basic mundane things (on which more excting and less mundane things can be built) that are not getting done. Robert On Wed, Oct 27, 2004 at 01:36:18PM -0700, jeffrey rasmussen wrote: > Using GO 1.6.5 the following code produces a list of GO terms that are > annotated as being connected with a certain LL id, but have their > "Ontology" slot listed as "NA" (presumably because they are missing from > GOTERM and the other GO* objects): > > library(GO) > ll2go <- as.list.environment(GOLOCUSID2GO) > tmp <- lapply(ll2go, function (x) sapply(x, function(x) > ifis.na(x$Ontology)){ print(x$GOID) })) > > Perhaps a more recent file was used to build GOLOCUSID2GO than was used to > build the remaining GO annotations? > > Jeff. > > (Here's the list of missing terms) > > GO:0001880 > GO:0001881 > GO:0001883 > GO:0001886 > GO:0030968 > GO:0030970 > GO:0030971 > GO:0035199 > GO:0035211 > GO:0035214 > GO:0035215 > GO:0035224 > GO:0035226 > GO:0035227 > GO:0035229 > GO:0035232 > GO:0035233 > GO:0035234 > GO:0043185 > GO:0043190 > GO:0043197 > GO:0043198 > GO:0048488 > GO:0048489 > GO:0051082 > GO:0051087 > GO:0051089 > GO:0051092 > GO:0051097 > GO:0051101 > GO:0051106 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------ + | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------ + ------------------------------ Message: 15 Date: Thu, 28 Oct 2004 00:05:27 -0700 From: Byron Ellis <bellis@hsph.harvard.edu> Subject: Re: [BioC] Problem installing graph package To: Robert Gentleman <rgentlem@jimmy.harvard.edu> Cc: bioconductor@stat.math.ethz.ch Message-ID: <bf340e92-28af-11d9-b678-000d93c24d64@hsph.harvard.edu> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Subscribing to the Mac SIG mailing list might also be a good idea, it can be really useful when g77 goes weird on you. Oh, and the repository version of Ruuid doesn't require glib on OS X (sort of a heavy requirement for something like 5 typedefs), you might try building that version instead. On Oct 27, 2004, at 11:44 AM, Robert Gentleman wrote: > Hi, > First your real problem is that you do not have Ruuid installed (and > that is what graph reports as the problem). So that would be your > first port of call. There are some details of how to do this, and > what libraries you need in the mailing list archives. > > so do install.packages2("Ruuid") > and then see what libraries you do not have installed on your system, > then get them and install them. > > Second, you do not have g77, so you won't be able to install any > fortran code (and that is what is in hexbin). Again, this is because > you lack the right tools in OS X, so you need to find them and > install them. Stefano Iacus keeps a nice web page that describes what > you need to have installed etc. for building R packages. The OS X > FAQ, is another place to look for details (and probably the first > place to look), > > Best > Robert > > On Wed, Oct 27, 2004 at 02:28:50PM -0400, Matt McCall wrote: >> Using R v2.0.0 on MacOS X in the R console. >> I was able to install most of bioconductor. I wanted to use the >> GOstats >> package (amoung a few others), and it didn't install properly. So I >> went back to try to find the problem, and it seems that the graph >> package isn't installing. Any suggestions? >> Matt >> >>> getBioC("prog", develOK=T) >> Running getBioC version 1.2.66.... >> If you encounter problems, first make sure that >> you are running the latest version of getBioC() >> which can be found at: www.bioconductor.org/getBioC.R >> >> Please direct any concerns or questions to >> bioconductor@stat.math.ethz.ch. >> >> Please select an installation directory: >> 1:/Users/mmccall/Library/R/library >> 2:/Library/Frameworks/R.framework/Resources/library >> Selection: 1 >> [1] "Attempting to download graph from >> http://www.bioconductor.org/repository/devel/package/Source" >> [1] "Download complete." >> [1] "Installing graph" >> * Installing *source* package 'graph' ... >> ** libs >> gcc -no-cpp-precomp >> -I/Library/Frameworks/R.framework/Resources/include >> -I/usr/local/include -fno-common -g -O2 -c graph.c -o graph.o >> graph.c: In function `intersectStrings': >> graph.c:39: warning: assignment makes pointer from integer without a >> cast >> graph.c:56: warning: assignment makes pointer from integer without a >> cast >> graph.c: In function `graphIntersection': >> graph.c:118: warning: assignment makes pointer from integer without a >> cast >> graph.c: In function `checkEdgeList': >> graph.c:157: warning: assignment makes pointer from integer without a >> cast >> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o >> graph.so graph.o -lcc_dynamic -framework R >> ld: warning multiple definitions of symbol _xerbla_ >> /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_ >> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ >> vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of >> _xerbla_ >> ld: warning multiple definitions of symbol _crc32 >> /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32 >> /usr/lib/libz.1.dylib(crc32.o) definition of _crc32 >> ld: warning multiple definitions of symbol _get_crc_table >> /Library/Frameworks/R.framework/R(crc32.lo) definition of >> _get_crc_table >> /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table >> ld: warning multiple definitions of symbol _deflate >> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflate >> ld: warning multiple definitions of symbol _deflateCopy >> /Library/Frameworks/R.framework/R(deflate.lo) definition of >> _deflateCopy >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy >> ld: warning multiple definitions of symbol _deflateReset >> /Library/Frameworks/R.framework/R(deflate.lo) definition of >> _deflateReset >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset >> ld: warning multiple definitions of symbol _deflateSetDictionary >> /Library/Frameworks/R.framework/R(deflate.lo) definition of >> _deflateSetDictionary >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary >> ld: warning multiple definitions of symbol _deflateInit2_ >> /Library/Frameworks/R.framework/R(deflate.lo) definition of >> _deflateInit2_ >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_ >> ld: warning multiple definitions of symbol _deflateEnd >> /Library/Frameworks/R.framework/R(deflate.lo) definition of >> _deflateEnd >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd >> ld: warning multiple definitions of symbol _deflateParams >> /Library/Frameworks/R.framework/R(deflate.lo) definition of >> _deflateParams >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams >> ld: warning multiple definitions of symbol _deflateInit_ >> /Library/Frameworks/R.framework/R(deflate.lo) definition of >> _deflateInit_ >> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_ >> ld: warning multiple definitions of symbol _zError >> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError >> /usr/lib/libz.1.dylib(zutil.o) definition of _zError >> ld: warning multiple definitions of symbol _zlibVersion >> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion >> /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion >> ld: warning multiple definitions of symbol _inflateEnd >> /Library/Frameworks/R.framework/R(inflate.lo) definition of >> _inflateEnd >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd >> ld: warning multiple definitions of symbol _inflateSync >> /Library/Frameworks/R.framework/R(inflate.lo) definition of >> _inflateSync >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync >> ld: warning multiple definitions of symbol _inflateSyncPoint >> /Library/Frameworks/R.framework/R(inflate.lo) definition of >> _inflateSyncPoint >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint >> ld: warning multiple definitions of symbol _inflate >> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflate >> ld: warning multiple definitions of symbol _inflateSetDictionary >> /Library/Frameworks/R.framework/R(inflate.lo) definition of >> _inflateSetDictionary >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary >> ld: warning multiple definitions of symbol _inflateInit2_ >> /Library/Frameworks/R.framework/R(inflate.lo) definition of >> _inflateInit2_ >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_ >> ld: warning multiple definitions of symbol _inflateReset >> /Library/Frameworks/R.framework/R(inflate.lo) definition of >> _inflateReset >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset >> ld: warning multiple definitions of symbol _inflateInit_ >> /Library/Frameworks/R.framework/R(inflate.lo) definition of >> _inflateInit_ >> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_ >> ld: warning multiple definitions of symbol _adler32 >> /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32 >> /usr/lib/libz.1.dylib(adler32.o) definition of _adler32 >> ld: warning multiple definitions of symbol _BC >> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ >> libreadline.4.3.dylibterminal.so) definition of _BC >> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC >> ld: warning multiple definitions of symbol _UP >> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ >> libreadline.4.3.dylibterminal.so) definition of _UP >> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP >> ld: warning multiple definitions of symbol _PC >> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ >> libreadline.4.3.dylibterminal.so) definition of _PC >> /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC >> ld: warning multiple definitions of symbol _gzeof >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzeof >> ld: warning multiple definitions of symbol _gzclose >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzclose >> ld: warning multiple definitions of symbol _gzdopen >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen >> ld: warning multiple definitions of symbol _gzerror >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzerror >> ld: warning multiple definitions of symbol _gzflush >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzflush >> ld: warning multiple definitions of symbol _gzgetc >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc >> ld: warning multiple definitions of symbol _gzgets >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgets >> ld: warning multiple definitions of symbol _gzopen >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzopen >> ld: warning multiple definitions of symbol _gzprintf >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf >> ld: warning multiple definitions of symbol _gzputc >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputc >> ld: warning multiple definitions of symbol _gzputs >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputs >> ld: warning multiple definitions of symbol _gzread >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzread >> ld: warning multiple definitions of symbol _gzrewind >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind >> ld: warning multiple definitions of symbol _gzseek >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzseek >> ld: warning multiple definitions of symbol _gzsetparams >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams >> ld: warning multiple definitions of symbol _gztell >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell >> /usr/lib/libz.1.dylib(gzio.o) definition of _gztell >> ld: warning multiple definitions of symbol _gzwrite >> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite >> /usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite >> ** R >> ** data >> ** inst >> ** save image >> [1] TRUE >> [1] TRUE >> [1] TRUE >> Loading required package: cluster >> Loading required package: Biobase >> Loading required package: tools >> Welcome to Bioconductor >> Vignettes contain introductory material. To view, >> simply type: openVignette() >> For details on reading vignettes, see >> the openVignette help page. >> [1] "propertyHolder" >> [1] "property" >> [1] "property" >> [1] "property<-" >> [1] "property<-" >> [1] "asGraphProperty" >> [1] "asGraphProperty" >> [1] "asGraphProperty" >> [1] "asGraphProperty" >> [1] "asGraphProperty" >> [1] "graph" >> [1] "edgemode" >> [1] "edgemode" >> [1] "edgemode<-" >> [1] "edgemode<-" >> [1] "graphNEL" >> [1] "initialize" >> [1] "nodes" >> [1] "nodes" >> [1] "nodes<-" >> [1] "nodes<-" >> [1] "edges" >> [1] "edges" >> [1] "edges" >> [1] "degree" >> [1] "degree" >> [1] "degree" >> [1] "edgeWeights" >> [1] "edgeWeights" >> [1] "adj" >> [1] "adj" >> [1] "acc" >> [1] "acc" >> [1] "DFS" >> [1] "DFS" >> [1] "edgeL" >> [1] "edgeL" >> [1] "subGraph" >> [1] "subGraph" >> [1] "intersection2" >> [1] "intersection2" >> [1] "intersection" >> [1] "intersection" >> [1] "join" >> [1] "join" >> [1] "union" >> [1] "union" >> [1] "complement" >> [1] "complement" >> [1] "connComp" >> [1] "connComp" >> [1] "isConnected" >> [1] "isConnected" >> [1] "numNodes" >> [1] "numNodes" >> [1] "numNodes" >> [1] "addNode" >> [1] "addNode" >> [1] "addNode" >> [1] "removeNode" >> [1] "removeNode" >> [1] "clearNode" >> [1] "clearNode" >> [1] "removeEdge" >> [1] "removeEdge" >> [1] "addEdge" >> [1] "addEdge" >> [1] "combineNodes" >> [1] "combineNodes" >> [1] "inEdges" >> [1] "inEdges" >> [1] "inEdges" >> [1] "inEdges" >> [1] "show" >> [1] "edgeNames" >> [1] "edgeNames" >> [1] "clusteringCoefficient" >> [1] "clusteringCoefficient" >> Error in assign("nullgraphID", getuuid()) : >> couldn't find function "getuuid" >> Execution halted >> cat: ** Removing '/Users/mmccall/Library/R/library/graph' >> ** Restoring previous '/Users/mmccall/Library/R/library/graph' >> stdout: Broken pipe >> ERROR: execution of package source for 'graph' failed >> [1] "Attempting to download hexbin from >> http://www.bioconductor.org/repository/devel/package/Source" >> [1] "Download complete." >> [1] "Installing hexbin" >> * Installing *source* package 'hexbin' ... >> ** libs >> g77 -fno-common -g -O2 -c hbin.f -o hbin.o >> ** Removing '/Users/mmccall/Library/R/library/hexbin' >> make: g77: Command not found >> make: *** [hbin.o] Error 127 >> ERROR: compilation failed for package 'hexbin' >> ** Restoring previous '/Users/mmccall/Library/R/library/hexbin' >> [1] "Attempting to download Ruuid from >> http://www.bioconductor.org/repository/devel/package/Source" >> [1] "Download complete." >> [1] "Installing Ruuid" >> * Installing *source* package 'Ruuid' ... >> creating cache ./config.cache >> checking for glib-config... no >> checking how to run the C preprocessor... cc -E >> checking for /usr/include/unistd.h... yes >> updating cache ./config.cache >> creating ./config.status >> creating src/Makevars >> ** libs >> gcc -no-cpp-precomp >> -I/Library/Frameworks/R.framework/Resources/include >> -I/usr/local/include/glib12 -DHAVE_UNISTD_H=1 -I/usr/local/include >> -fno-common -g -O2 -c Rinit.c -o Rinit.o >> In file included from Ruuid.h:5, >> from Rinit.c:1: >> uuidP.h:24:18: glib.h: No such file or directory >> In file included from Ruuid.h:5, >> from Rinit.c:1: >> uuidP.h:36: error: parse error before "guint32" >> uuidP.h:36: warning: no semicolon at end of struct or union >> uuidP.h:37: warning: data definition has no type or storage class >> uuidP.h:38: error: parse error before "time_hi_and_version" >> uuidP.h:38: warning: data definition has no type or storage class >> uuidP.h:39: error: parse error before "clock_seq" >> uuidP.h:39: warning: data definition has no type or storage class >> uuidP.h:40: error: parse error before "node" >> uuidP.h:40: warning: data definition has no type or storage class >> uuidP.h:41: error: parse error before '}' token >> ** Removing '/Users/mmccall/Library/R/library/Ruuid' >> ** Restoring previous '/Users/mmccall/Library/R/library/Ruuid' >> make: *** [Rinit.o] Error 1 >> ERROR: compilation failed for package 'Ruuid' >> From URL: >> http://www.bioconductor.org/repository/devel/package/Source >> graph version 1.4.22 >> hexbin version 1.1-2 >> Ruuid version 1.4.5 >> >> Packages Rgraphviz and rhdf5 require special libraries to be >> installed. >> Please see the URL http://www.bioconductor.org/faq.html#Other Notes >> for >> more details on installing these packages if they fail >> to install properly >> >> Warning messages: >> 1: Installation of package graph had non-zero exit status in: >> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) >> 2: Installation of package hexbin had non-zero exit status in: >> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) >> 3: Installation of package Ruuid had non-zero exit status in: >> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > -- > +------------------------------------------------------------------- --- > -----+ > | Robert Gentleman phone : (617) 632-5250 > | > | Associate Professor fax: (617) 632-2444 > | > | Department of Biostatistics office: M1B20 > | > | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu > | > +------------------------------------------------------------------- --- > -----+ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > --- Byron Ellis (ellis@stat.harvard.edu) "Oook" -- The Librarian ------------------------------ Message: 16 Date: Thu, 28 Oct 2004 10:33:47 +0200 From: Martin Maechler <maechler@stat.math.ethz.ch> Subject: Re: [BioC] Color in the lefs of a dendrogram? To: "Johan Lindberg" <johanl@biotech.kth.se> Cc: bioconductor@stat.math.ethz.ch Message-ID: <16768.44779.879793.334930@gargle.gargle.HOWL> Content-Type: text/plain; charset=us-ascii Y >>>>> "Johan" == Johan Lindberg <johanl@biotech.kth.se> >>>>> on Wed, 27 Oct 2004 10:14:57 +0200 writes: Johan> Hi all. I have a question of how to put color in a plot of a Johan> hierarchical clustering that I have done with 24 microarrays in an Johan> experiment. The basic code that I use to plot: Johan> sampdist <- dist(t(Mmatrix), method="euclidean") Johan> sclus <- hclust(sampdist, method="average") Johan> plot(sclus, cex=0.7) Use dclus <- as.dendrogram(sclus) and -- after reading help(dendrogram) and maybe executing example(dendrogram) use plot(dclus, ......................) Martin Maechler, ETH Zurich ------------------------------ Message: 17 Date: Thu, 28 Oct 2004 10:42:52 +0200 From: Binita Dutta <binita.dutta@vib.be> Subject: [BioC] Comparison of Affymetrix and CodeLink chip To: bioconductor@stat.math.ethz.ch Message-ID: <6.0.0.22.1.20041028104202.01ebd468@194.78.28.203> Content-Type: text/plain; charset="us-ascii"; format=flowed Dear All, I have been using limma for data analysis of affymetrix chips. We want to compare result of affymetrix chip and Amersham Codelink. We have done experiment with three knock out mice and compared with the wild type mice. Can you suggest us the best bioconductor packages which can be used to fish out differentially experessed genes with P. values on affymetrix and codelink slides. Help in this regard will be highly appreciated. Binita ============================== Binita Dutta, PhD MicroArray Facility(MAF) UZ Gasthuisberg Onderwijs en Navorsing Herestraat 49 3000 Leuven Belgium ------------------------------ _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor End of Bioconductor Digest, Vol 20, Issue 27