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Hi Henrik, No.. I did not manage to build an annotaiton package of the affymetrix porcine chip, although I considered using the BLAST orthologes available at affymetrix.com, as input to AnnBuilder. My impression is that pig genes have surprisingly very poor annotaiton in public databases and doing micoarray on pig must be very frustrating, despite its close relationship to human. The annotaiton provided by Affymetrix also suck. (cdf file & NetAffy.) The BLAST orthologes or Homologene could be a fruitful.. or maybe biomaRt & getHomolog good luck, and mail us if you succeed :) regards morten Henrik Hornsh?j Jensen wrote: >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:bioco nductor%40stat.math.ethz.ch?subject="%5BBioC%5D%20affymetrix%20pig%20an" notation%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]] > > > >--------------------------------------------------------------------- --- > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > >