search for: annbuilder

Hi there. I got some Problems building an Annotation-Package with AnnBuilder. Not using the function ABPkgBuilder(), but just parts of it to create a package without connecting to the servers, I managed to create a Package, but it seems to be empty. R recognizes it as a package, but is unable to load it. The form of the data is in a correct form, I got an example-annotat...

Hallo everybody. I want to build my own GO package using the function GOPkgBuilder of AnnBuilder. It uses AnnBuilderSourceUrls to collect data from different ftp sites. These data are not complete for my organism, so I would like to change the ftp adresses to a local one. The changing itself is working but when I run the script I get the following Error: Error in loadFromUrl(file.path(sourceU...

...of MAS 5.0 now agrees better with Affymetrix's then in previous releases, and now includes a function mas5() to make it easier for a user to obtain these results. * affycomp: A new package that serves as a graphics toolbox for the assessment of Affymetrix expression measures. * AnnBuilder: DB support is no longer required. ABPkgBuilder now provides a signle API for building of data packages. Also, data packages built with AnnBuilder will include an evidence code and association information for GO ids. * Biobase: The exprs2excel method for the exprSet class has been adde...

Hi How do I install "gregmisc" packages? I did- % sudo R > install.packages("gregmisc") . . > barplot2() but, Error: couldn't find function "barplot2" -- atuya Mac OSX 10.2.6 R 1.7.1

...llo! I don't know if there is some R-package able to associate ontology to a long list of GeneBank Name (a txt-tab file or an XML file), i.e. I would as output a formatted file with 4 columns (1:GeneBank Name 2,3,4:ontology). I know that I have to perform a mapping of genes, I got a look on AnnBuilder pkg, but I 've not idea from where to start. Some suggestion? Thanks in advance! A. S.

...know. RXLisp does not compile any more. what builds -- Everything from CRAN, including RMySQL, RmSQL, XML, rpvm, rsprng, RMpi, but not ROracle, RSQLite, RQuantlib -- Lindsay packages rmutil, gnlm, stable, growthm repeated, event, ordinal -- Bioconductor packages Biobase, annotate, affy, AnnBuilder, edd, genefilter, geneplotter, rhdf5, marrayTest, marrayClasses, marrayInput, marrayPlots, multtest, ROC, tkWidgets -- snow from Tierney -- deal from gR -- from Devel Dopt, GRASS, PHYLOGR, R2HTML, RPgSQL, dseplus, pls, runstat, multidim, mclust, ensemble, locfit, write-snns -- from OmegaHa...

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

.... Re: Does anyone else think this might be worth a warning?!? (Felix Andrews) 31. Re: how to collapse a list of 1 column matrix to a matrix? (Fran?ois Pinard) 32. Re: how to collapse a list of 1 column matrix to a matrix? (adschai at optonline.net) 33. Building Packages with AnnBuilder (jakob bleier) 34. Differentiation (Shubha Vishwanath Karanth) 35. Labelling certain points on the x-axis (squall44) 36. Re: Restricted VAR parameter estimation (Pfaff, Bernhard Dr.) 37. Re: Differentiation (Uwe Ligges) 38. Question about writing some code (squall44) 39. Re: Building Pa...

...;. --- vsn: Two new functions were added 'sagmbSimulateData' and 'sagmbAssess' to quantitatively verify finite sample properties and outlier robustness of the parameter estimation in vsn(). -- TOOLS: The released packages include tools which facilitate: * annotation (AnnBuilder, annotate). * data management and organization through the use of the S4 class structure (Biobase, marrayClasses, limma). * identification of differentially expressed genes and clustering (edd, genefilter, geneplotter, multtest, ROC, limma) * analysis of Affymetrix expression array data...

...;. --- vsn: Two new functions were added 'sagmbSimulateData' and 'sagmbAssess' to quantitatively verify finite sample properties and outlier robustness of the parameter estimation in vsn(). -- TOOLS: The released packages include tools which facilitate: * annotation (AnnBuilder, annotate). * data management and organization through the use of the S4 class structure (Biobase, marrayClasses, limma). * identification of differentially expressed genes and clustering (edd, genefilter, geneplotter, multtest, ROC, limma) * analysis of Affymetrix expression array data...

Dear All, I have a question regarding best practise in setting up a XML parser within R. Because I have files with more than 100 MB and I'm only interested in some values I think a SAX-like parser using xmlEventParse() will be the best solution. Unfortunately the values I'm looking for, to construct some higher "mass spectrum", are distributed over different lines: as

I've for a RHEL 4 box on a P570 system. My end user wants to have a 64-bit version of R compiled due to the large amount of memory they require (this image has 16GB allocated to it). I can compile R fine in 32-bit mode, but it can't use more than 2.4GB of RAM before it falls over and dies. Compiling in 64-bit mode for POWER systems "should" be as easy as adding a