Hi Ting-Yuan, I am happy you and the other authors are making mu11ksuba and mu11ksubb for 1.8 soon. If you would send me these two, I would love to test them. Meanwhile, I would like to get ABPkgBuilder working. myBaseType="ug". Do you need to have values for the otherSrc argument? Thanks very much for your help, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ********* On Thu, 23 Mar 2006, Ting-Yuan Liu wrote: > > Hi Dick, > > A quick question: what is the "myBaseType" value for the argument > baseMapType? It should be "ug" because your basefile is the mapping > between probe ids and unigene ids. > > From the information you provided, it is difficult for me to figure out > where the problem is. We are going to release mu11ksuba and mu11ksubb for > the BioC 1.8, and I have built these two packages successfully. We are > testing them now and will put them on the repository for users to test > soon. In case you are still interested in building your own mu11ksuba, > here are the code I used to build it: > > > ABPkgBuilder(baseName="mu11ksuba.GeneBankID", > baseMapType="gbNRef", > pkgName="mu11ksuba", > pkgPath=".", > organism="Mus musculus", > otherSrc=c( > EG="mu11ksuba.EntrezGeneID", > UG="mu11ksuba.UniGeneID" > ), > version="1.11.20", > author=list( > authors="Ting-Yuan Liu, ChenWei Lin, Seth Falcon, > Jianhua Zhang, James W. MacDonald", > maintainer="Ting-Yuan Liu <tliu at="" fhcrc.org="">" > ) > ) > > where > > mu11ksuba.GeneBankID: > aa000148_s_at AA000148 > AA000151_at AA000151 > aa000380_s_at AA000380 > aa000467_s_at AA000467 > aa000469_at AA000469 > ... > > mu11ksuba.EntrezGeneID: > aa000148_s_at 66164 > AA000151_at 67467 > aa000380_s_at 230908 > aa000467_s_at 66119 > aa000469_at 11772 > ... > > mu11ksuba.UniGeneID: > aa000148_s_at Mm.334789 > AA000151_at Mm.260767 > aa000380_s_at Mm.22453 > aa000467_s_at Mm.188339 > aa000469_at Mm.253090 > ... > > You can parse these mappings from the annotation file Affymetrix provides. > > HTH, > Ting-Yuan > ______________________________________ > Ting-Yuan Liu > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > Seattle, WA, USA > ______________________________________ > > On Wed, 22 Mar 2006, Dick Beyer wrote: > >> I am having difficulty building a metadata package for mu11ksuba and was >> hoping someone would look at the error message and give me some suggestions as >> to what I am doing wrong. I am trying to follow the example in ABPrimer.pdf. >> >> sessionInfo() >> R version 2.2.1, 2005-12-20, x86_64-unknown-linux-gnu >> >> attached base packages: >> [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" >> [7] "datasets" "base" >> >> other attached packages: >> AnnBuilder annotate XML limma siggenes qvalue >> "1.8.0" "1.8.0" "0.99-6" "2.4.11" "1.4.0" "1.4.0" >> gcrma matchprobes annaffy KEGG GO affy >> "2.2.1" "1.2.1" "1.2.0" "1.8.1" "1.8.2" "1.8.1" >> Biobase >> "1.8.0" >> >> >> myBase <- read.table("/home/dbeyer/Microarray/affy resourcerer >> files/affy_Mu11KA UG for AnnBuilder.txt",sep = "\t", header = FALSE, as.is = >> TRUE) >> >>> myBase[1:5,] >> V1 V2 >> 1 AA000151_at Mm.260767 >> 2 AA004127_at Mm.3819 >> 3 AA009039_at Mm.35837 >> 4 AA014405_at Mm.29677 >> 5 AA014745_at Mm.275414 >> >> mySrcUrls <- getOption("AnnBuilderSourceUrls") >>> mySrcUrls >> $EG >> [1] "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA" >> $GEO >> [1] "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?" >> $GO >> [1] "http://www.godatabase.org/dev/database/archive/latest" >> $GP >> [1] "ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes" >> $HG >> [1] "ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp" >> $KEGG >> [1] "ftp://ftp.genome.ad.jp/pub/kegg/pathways" >> $LL >> [1] "ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz" >> $UG >> [1] "ftp://ftp.ncbi.nih.gov/repository/UniGene" >> $YG >> [1] "ftp://genome-ftp.stanford.edu/pub/yeast/data_download/" >> $AT >> [1] "ftp://ftp.arabidopsis.org/home/tair/" >> $IPI >> [1] "ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/" >> $CMAP >> [1] "ftp://ftp1.nci.nih.gov/pub/CMAP/" >> >> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, >> pkgName = "mu11ksuba", pkgPath = ".", organism = "Mus musculus", version = >> "1.0", author = list(author = "dbeyer", maintainer = >> "dbeyer at u.washington.edu"), fromWeb = TRUE) >> >> Error in validObject(.Object) : invalid class "EG" object: invalid object for >> slot "baseFile" in class "EG": got class "data.frame", should be or extend >> class "character" >> >> Thanks very much for any help or suggestions, >> Dick >> ******************************************************************* ************ >> Richard P. Beyer, Ph.D. University of Washington >> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 >> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 >> Seattle, WA 98105-6099 >> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html >> http://staff.washington.edu/~dbeyer >> >> _______________________________________________ >> 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 >> >