Hi Yongde Bao, There is a new package xps in the Devel repository that is intended for the analysis of the gene arrays. To use this package you will need R-devel, as well as installing ROOT. There are clear instructions for building the package on *NIX as well as MacOSX, but if you want to run on Windows you will have to figure things out for yourself. In addition, someone has already posted links to cdf packages for this chip that will allow you to use the affy package. Note however that some of the probes on this chip are shared between probesets, and that was not true in the past, so for a certain percentage of probesets you will be missing probes (once a probe is allocated to a probeset, it will not be available for any other probesets). Best, Jim Yongde Bao wrote: > Hi all, > > I wonder if there is any package in Bioconductor that deals with the analysis > of the Affy Human ST gene arrays. If so can someone point out where to get it? > > Best regards, > > Yongde Bao > University of Virginia > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

Dear Yongde As James MacDonald has already kindly mentioned, my package xps is able to handle both Affymetrix HuGene and Exon arrays. Is has no problems with shared probesets, and you can do RMA and MAS5 normalization. Please note that you can use xps with both R-2.5.0 and R-2.6.0 so you need not install R-devel. If you are willing to install and try it I would appreciate any feedback. Best regards Christian _._._._._._._._._._._._._._._._ C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._ Yongde Bao wrote: > Hi all, > > I wonder if there is any package in Bioconductor that deals with the analysis > of the Affy Human ST gene arrays. If so can someone point out where to get it? > > Best regards, > > Yongde Bao > University of Virginia > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >

Hi Tony, I'm sorry, but for now, we cannot update the R and BioC versions. R is installed on a sparc-sun-solaris server for all our applications. And it's always complicated, for all developers and application users, to make this type of update. Moreover, i'm not convinced that it could resolve the probleme ... Thanks for your help, Best, Nicolas Tony Chiang wrote: > Hi Nicolas, > > Can you try and update your R to 2.6 and your Bioc to 2.2 to see if this > problem still persists? > Or is there a reason you are using the old versions of R and Bioc? > > Best, > --Tony > > On 10/26/07, Nicolas Servant <nicolas.servant at="" curie.fr=""> wrote: > >> Hi, >> >> I try to install the GoStats (BioC 2.0, GoStat.2.2.6) package on R >> 2.5.1, but I have some C++ compilation errors due to RBGL package. >> The errors are link to the boost library and namespace definition. >> Does anybody have an idea ? >> >> >> >>> sessionInfo() >>> >> R version 2.5.1 (2007-06-27) >> sparc-sun-solaris2.9 >> >> Error : >> * checking for file 'RBGL/DESCRIPTION' ... OK >> * preparing 'RBGL': >> * checking DESCRIPTION meta-information ... OK >> * cleaning src >> * running cleanup >> removing exploded boost header source... >> * installing the package to re-build vignettes >> * Installing *source* package 'RBGL' ... >> untarring boost include tree... >> ** libs >> /opt/SUNWspro/bin/CC -xO5 -xdepend -xlic_lib=sunperf -xmemalign=8s >> -xprefetch=auto,explicit -xtarget=native -lCstd >> -I/bioinfo/local/SunR/lib/R/include -I/bioinfo/local/SunR/lib/R/include >> -I/usr/local/include -IboostIncl -KPIC -O -c bbc.cpp -o bbc.o >> CC: Warning: -O overwrites previously set optimization level of -O5 >> CC: Warning: -xarch=native has been explicitly specified, or implicitly >> specified by a macro option, -xarch=native on this architecture implies >> -xarch=v8plusb which generates code that does not run on pre UltraSPARC >> III processors >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 439: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> >> boost::ID>(std::vector<boost::detail::edge_desc_impl<boost::undirec ted_tag,="">> unsigned> >*, >> ........ >> boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_ind ex_t,="">> int, boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>). >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> While instantiating >> >> "boost::detail::graph::brandes_betweenness_centrality_dispatch2<boo st::adjacency_list<boost::vecs,="">> >> ........ >> boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> ......... >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 440: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> boost::ID>(double*, >> .......... >> boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> ............ >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> .............. >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 441: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> boost::ID>(double*, boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> .............. >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 442: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> boost::ID>(unsigned*, >> .................. >> boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> ............. >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> 4 Error(s) detected. >> make: *** [bbc.o] Error 4 >> >> >> Thanks for your help, >> Regards, >> >> Nicolas. >> >> >> -- >> Nicolas Servant >> Equipe Bioinformatique >> Institut Curie >> 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE >> >> Email: Nicolas.Servant at curie.fr >> Tel: 01 53 10 70 55 >> http://bioinfo.curie.fr/ >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > . > > -- Nicolas Servant Equipe Bioinformatique Institut Curie 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE Email: Nicolas.Servant at curie.fr Tel: 01 53 10 70 55 http://bioinfo.curie.fr/

Hi, 1- RBGL_1.12.0.tar.gz form BioC2.0 2- CC: Sun C++ 5.8 Patch 121017-11 2007/05/02 This is the first time we use the Sun CC for R installation. The last time we used the g++ compiler without any probleme. Thanks Nicolas Li.Long at isb-sib.ch wrote: > Hi, > > First question: when and how you got the "RBGL"? > Second: what's your CC version? Did you install RBGL with it successfully > before? Or it's brandnew experience? The error msgs are about C++ > template handling. > > Thanks > > Li > > > >> Hi, >> >> I try to install the GoStats (BioC 2.0, GoStat.2.2.6) package on R >> 2.5.1, but I have some C++ compilation errors due to RBGL package. >> The errors are link to the boost library and namespace definition. >> Does anybody have an idea ? >> >> >> > sessionInfo() >> R version 2.5.1 (2007-06-27) >> sparc-sun-solaris2.9 >> >> Error : >> * checking for file 'RBGL/DESCRIPTION' ... OK >> * preparing 'RBGL': >> * checking DESCRIPTION meta-information ... OK >> * cleaning src >> * running cleanup >> removing exploded boost header source... >> * installing the package to re-build vignettes >> * Installing *source* package 'RBGL' ... >> untarring boost include tree... >> ** libs >> /opt/SUNWspro/bin/CC -xO5 -xdepend -xlic_lib=sunperf -xmemalign=8s >> -xprefetch=auto,explicit -xtarget=native -lCstd >> -I/bioinfo/local/SunR/lib/R/include -I/bioinfo/local/SunR/lib/R/include >> -I/usr/local/include -IboostIncl -KPIC -O -c bbc.cpp -o bbc.o >> CC: Warning: -O overwrites previously set optimization level of -O5 >> CC: Warning: -xarch=native has been explicitly specified, or implicitly >> specified by a macro option, -xarch=native on this architecture implies >> -xarch=v8plusb which generates code that does not run on pre UltraSPARC >> III processors >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 439: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> boost::ID>(std::vector<boost::detail::edge_desc_impl<boost::undirec ted_tag,="">> unsigned> >*, >> ........ >> boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_ind ex_t,="">> int, boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>). >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> While instantiating >> "boost::detail::graph::brandes_betweenness_centrality_dispatch2<boo st::adjacency_list<boost::vecs,="">> >> ........ >> boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> ......... >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 440: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> boost::ID>(double*, >> .......... >> boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> ............ >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> .............. >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 441: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> boost::ID>(double*, boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> .............. >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 442: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> boost::ID>(unsigned*, >> .................. >> boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> ............. >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> 4 Error(s) detected. >> make: *** [bbc.o] Error 4 >> >> >> Thanks for your help, >> Regards, >> >> Nicolas. >> >> >> -- >> Nicolas Servant >> Equipe Bioinformatique >> Institut Curie >> 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE >> >> Email: Nicolas.Servant at curie.fr >> Tel: 01 53 10 70 55 >> http://bioinfo.curie.fr/ >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > > . > > -- Nicolas Servant Equipe Bioinformatique Institut Curie 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE Email: Nicolas.Servant at curie.fr Tel: 01 53 10 70 55 http://bioinfo.curie.fr/