Hi, I am having a problem with AnnBuilder: Error in "[.data.frame"(annotation, , 1:3) : undefined columns selected The code that generate this error is below: > myBase <- "ProbeIdToLL.txt" > myBaseType <- "ll" > myDir <- tempdir() > mySrcUrls <- getSrcUrl("all", "Mus musculus") > ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, pkgName = "agilentOligo", pkgPath = myDir, organism = "Mus musculus", version = "1.1.0", author = list(author = "sylvain", maintainer = "sylvain at sdsc.edu"), fromWeb = TRUE) Error in "[.data.frame"(annotation, , 1:3) : undefined columns selected In addition: Warning message: Built for UCSC is not valid! in: getUCSCBuilt(organism) > sessionInfo() R version 2.2.0, 2005-10-06, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" other attached packages: GO AnnBuilder annotate XML Biobase "1.10.0" "1.8.0" "1.8.0" "0.99-5" "1.8.0" Thanks. Sylvain

Hi Sylvain, Could you remove the argument "srcUrls = mySrcUrls" and try again? ABPkgBuilder will find the srcUrls automatically. If this cannot solve the problem, you can send me the "ProbeIdToLL.txt" file and I am happy to test it for you. Moreover, the argument author should be author = list(authors = "sylvain", maintainer = "sylvain <sylvain at="" sdsc.edu="">") See the difference? HTH, Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA ______________________________________ On Fri, 20 Jan 2006, Sylvain Pradervand wrote: > > Hi, > > I am having a problem with AnnBuilder: > > Error in "[.data.frame"(annotation, , 1:3) : > undefined columns selected > > The code that generate this error is below: > > > myBase <- "ProbeIdToLL.txt" > > myBaseType <- "ll" > > myDir <- tempdir() > > mySrcUrls <- getSrcUrl("all", "Mus musculus") > > ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = > myBaseType, pkgName = "agilentOligo", pkgPath = myDir, organism = "Mus > musculus", version = "1.1.0", author = list(author = "sylvain", > maintainer = "sylvain at sdsc.edu"), fromWeb = TRUE) > > Error in "[.data.frame"(annotation, , 1:3) : > undefined columns selected > In addition: Warning message: > Built for UCSC is not valid! in: getUCSCBuilt(organism) > > > sessionInfo() > R version 2.2.0, 2005-10-06, i386-pc-mingw32 > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > "datasets" "base" > > other attached packages: > GO AnnBuilder annotate XML Biobase > "1.10.0" "1.8.0" "1.8.0" "0.99-5" "1.8.0" > > > Thanks. > > Sylvain > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >