AnnBuilder problem for mu11ksuba
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Dick Beyer ★ 1.4k
@dick-beyer-26
Last seen 8.1 years ago
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
Organism mu11ksuba annotate limma gcrma matchprobes annaffy AnnBuilder Organism mu11ksuba • 701 views
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@ting-yuan-liu-fhcrc-1221
Last seen 8.1 years ago
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 >
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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 >> >
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