I finally managed to put something together that works. My basefile contains pig probe IDs mapped to human accession IDs using blast: 100049 NM_005384.2 100053 NM_214393.1 100055 NM_006219.1 100057 NM_016593.3 The code is below. Henrik ######################################### library(AnnBuilder) myPkgName <- "PigArray" myBase <- "mybasefile.txt" myBaseRead <- read.table(myBase, sep = "\t", header = FALSE, as.is = TRUE) myBaseType <- "gbNRef" mySrcUrls <- getSrcUrl("all", "Homo sapiens") myDir <- "C:/PigArray" ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, pkgName = myPkgName, pkgPath = myDir, organism = "Homo sapiens", version = "2.0.0", author = list(author = "Henrik Hornshoj <henrikh.jensen at="" agrsci.dk="">", maintainer = "Henrik Hornshoj <henrikh.jensen at="" agrsci.dk="">"), fromWeb = TRUE) -----Oprindelig meddelelse----- Fra: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor- bounces at stat.math.ethz.ch] P? vegne af Henrik Hornsh?j Jensen Sendt: Tuesday, January 03, 2006 10:46 AM Til: bioconductor at stat.math.ethz.ch Emne: [BioC] affymetrix pig annotation data Dear Morten Mattingsdal Sorry to bother you with this, but I just wondered if you ever managed to solve you problem with building a data annotation package (see below)? I am trying to do something similiar, although not with an affy chip, and I get the same error as you: 'no direct or inherited method for function 'baseFile<-' for this call' Kind regards, Henrik Hornsh?j Department of Genetics and Biotechnology Danish Institute of Agricultural Sciences. [BioC] affymetrix pig annotation data Morten Mattingsdal morten.mattingsdal at student.uib.no <mailto:biocon ductor%40stat.math.ethz.ch?subject="%5BBioC%5D%20affymetrix%20pig%20ann" otation%20data&in-reply-to=""> Mon Nov 14 18:28:32 CET 2005 * Previous message: [BioC] Small bug in function 'countskip.FASTA.entries' from package 'altcdfenvs' <https: stat.ethz="" .ch="" pipermail="" bioconductor="" 2005-november="" 010955.html=""> * Next message: [BioC] gpr one color <https: stat.ethz.ch="" piper="" mail="" bioconductor="" 2005-november="" 010894.html=""> * Messages sorted by: [ date ] <https: stat.ethz.ch="" pipermail="" b="" ioconductor="" 2005-november="" date.html#10892=""> [ thread ] <https: stat.e="" thz.ch="" pipermail="" bioconductor="" 2005-november="" thread.html#10892=""> [ subject ] <https: stat.ethz.ch="" pipermail="" bioconductor="" 2005-november="" s="" ubject.html#10892=""> [ author ] <https: stat.ethz.ch="" pipermail="" biocond="" uctor="" 2005-november="" author.html#10892=""> ________________________________ Hello open-source spirits, Im trying to build an annotation data library for the Sus scrofa (common pig) affymetrix chip: GeneChip? Porcine Genome Array http://www.affymetrix.com/products/arrays/specific/porcine.affx but Im not very sucessful in doing so.. my error is Error in "baseFile<-"(`*tmp*`, value = "C:\\DOCUME~1\\mortema\\LOCALS~1\\Temp\\Rtmp2376\\tempFile26288") : no direct or inherited method for function 'baseFile<-' for this call and I dont know what this is trying so tell me. My imput is probe ID in coloum 1 and genbank acc.nr in coloum 2. "Ssc.11.1.S1_at" "NM_213802.1" and I have succesfully build packages before with human and mouse. But this is my first go at pig. Does anyone have this library already build or can someone help me build it ? (im deeply sorry if this is already listed in the metadata dir at bioconductor. But cant find anything related to pig) best morten [[alternative HTML version deleted]]