AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)
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Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 10.3 years ago
Hi, Weijun, The humanLLMappings package was generated by function map2LL rather than ABPkgBuilder, therefore it is a different case. I used ABPkgBuilder function generate a coupld of pakcages recently, and didn't see xxGENENAME or xxSYMBOL environments have any problem. So, I suspect the problem is specific to your input data. Could you please provide more details? e.g. myBaseType and maybe also a small part of myBase Also, you may want to upgrade AnnBuilder to 1.10.1. The UCSC Genome database updated their schema (one table) recently for human and mouse data, and AnnBuilder has been updated correspondingly. If you see problems with xxCHRLOC environment, please update your AnnBuilder. thanks nianhua Nianhua Li Computational Biology, PHS, FHCRC
AnnBuilder AnnBuilder • 1.1k views
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Luo Weijun ★ 1.6k
@luo-weijun-1783
Last seen 18 months ago
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Thank you so much, guys, For John??s question, My base map type is "ll", since my probes are mapped to Entrez Gene IDs directly. (please all see below for more details) For Nianhua??s question, below is all my codes for this work. library(AnnBuilder) load('/Users/luow/project/microarraydata/annotation/hs95av2Entrezg7.Rd ata') myBase=cbind(hs95av2Entrezg7,hs95av2Entrezg7) myBase[,1]=paste(hs95av2Entrezg7,'_at',sep='') write.table(myBase,file='/Users/luow/project/microarraydata/annotation /hs95av2Entrezg7Base.txt',sep='\t',row.names=F,col.names=F) myBase='/Users/luow/project/microarraydata/annotation/hs95av2Entrezg7B ase.txt' myBaseType <- "ll" myDir <- '/Users/luow/project/microarraydata/annotation/' ABPkgBuilder(baseName = myBase, baseMapType = myBaseType, pkgName = "hs95av2Entrezg7", pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", author = list(authors = "Weijun", maintainer = "Weijun <luo_weijun at="" yahoo.com="">"), fromWeb =T) Here is part of my base file: > a=read.delim('/Users/luow/project/microarraydata/annotation/hs95av2Ent rezg7Base.txt',sep='\t', head=F) > head(a) V1 V2 1 10001_at 10001 2 10002_at 10002 3 10003_at 10003 4 10004_at 10004 5 10005_at 10005 6 10006_at 10006 Here is what I got when I created and installed the package. And Nianhua is right, I got problem with hs95av2Entrezg7CHRLOC environment, no entry at all. I will need to update my AnnBuilder. But exactly how can I do that, using update.packages function or, is there anything for updating bioc packages specially? > library(hs95av2Entrezg7) > hs95av2Entrezg7() Quality control information for hs95av2Entrezg7 Date built: Created: Sat Jul 8 20:23:41 2006 Number of probes: 8359 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: hs95av2Entrezg7CHRLOC found 0 of 8359 hs95av2Entrezg7ENZYME found 1313 of 8359 hs95av2Entrezg7LOCUSID found 8292 of 8359 hs95av2Entrezg7PATH found 2784 of 8359 Mappings found for non-probe based rda files: hs95av2Entrezg7CHRLENGTHS found 25 hs95av2Entrezg7ENZYME2PROBE found 651 hs95av2Entrezg7ORGANISM found 1 hs95av2Entrezg7PATH2PROBE found 180 hs95av2Entrezg7PFAM found 6997 hs95av2Entrezg7PROSITE found 5451 Please let me know if you have any ideas, suggestions, or other questions. I really appreciate all the kind help you guys offer! Weijun --- Nianhua Li <nli at="" fhcrc.org=""> wrote: > Hi, Weijun, > > The humanLLMappings package was generated by > function map2LL rather than > ABPkgBuilder, therefore it is a different case. I > used ABPkgBuilder > function generate a coupld of pakcages recently, and > didn't see > xxGENENAME or xxSYMBOL environments have any > problem. So, I suspect the > problem is specific to your input data. Could you > please provide more > details? e.g. myBaseType and maybe also a small part > of myBase > Also, you may want to upgrade AnnBuilder to 1.10.1. > The UCSC Genome > database updated their schema (one table) recently > for human and mouse > data, and AnnBuilder has been updated > correspondingly. If you see > problems with xxCHRLOC environment, please update > your AnnBuilder. > > thanks > > nianhua > > Nianhua Li > Computational Biology, PHS, FHCRC > > _______________________________________________ > 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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Hello All, I posted this a couple of days ago, following some nice feedback. But haven't got further response yet, could anybody give me any suggestion/ideas on this problem? Thank you so much. Weijun --- Luo Weijun <luo_weijun at="" yahoo.com=""> wrote: Thank you so much, guys, For John's question, My base map type is "ll", since my probes are mapped to Entrez Gene IDs directly. For Nianhua's question, below is all my codes for this work. library(AnnBuilder) load('/Users/luow/project/microarraydata/annotation/hs95av2Entrezg7.Rd ata') myBase=cbind(hs95av2Entrezg7,hs95av2Entrezg7) myBase[,1]=paste(hs95av2Entrezg7,'_at',sep='') write.table(myBase,file='/Users/luow/project/microarraydata/annotation /hs95av2Entrezg7Base.txt',sep='\t',row.names=F,col.names=F) myBase='/Users/luow/project/microarraydata/annotation/hs95av2Entrezg7B ase.txt' myBaseType <- "ll" myDir <- '/Users/luow/project/microarraydata/annotation/' ABPkgBuilder(baseName = myBase, baseMapType = myBaseType, pkgName = "hs95av2Entrezg7", pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", author = list(authors = "Weijun", maintainer = "Weijun <luo_weijun at="" yahoo.com="">"), fromWeb =T) Here is part of my base file: > a=read.delim('/Users/luow/project/microarraydata/annotation/hs95av2Ent rezg7Base.txt',sep='\t', head=F) > head(a) V1 V2 1 10001_at 10001 2 10002_at 10002 3 10003_at 10003 4 10004_at 10004 5 10005_at 10005 6 10006_at 10006 Here is what I got when I created and installed the package. And Nianhua is right, I got problem with hs95av2Entrezg7CHRLOC environment, no entry at all. I will need to update my AnnBuilder. But exactly how can I do that, using update.packages function or, is there anything for updating bioc packages specially? > library(hs95av2Entrezg7) > hs95av2Entrezg7() Quality control information for hs95av2Entrezg7 Date built: Created: Sat Jul 8 20:23:41 2006 Number of probes: 8359 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: hs95av2Entrezg7CHRLOC found 0 of 8359 hs95av2Entrezg7ENZYME found 1313 of 8359 hs95av2Entrezg7LOCUSID found 8292 of 8359 hs95av2Entrezg7PATH found 2784 of 8359 Mappings found for non-probe based rda files: hs95av2Entrezg7CHRLENGTHS found 25 hs95av2Entrezg7ENZYME2PROBE found 651 hs95av2Entrezg7ORGANISM found 1 hs95av2Entrezg7PATH2PROBE found 180 hs95av2Entrezg7PFAM found 6997 hs95av2Entrezg7PROSITE found 5451 Please let me know if you have any ideas, suggestions, or other questions. I really appreciate all the kind help you guys offer! Weijun > > > --- Nianhua Li <nli at="" fhcrc.org=""> wrote: > > > Hi, Weijun, > > > > The humanLLMappings package was generated by > > function map2LL rather than > > ABPkgBuilder, therefore it is a different case. I > > used ABPkgBuilder > > function generate a coupld of pakcages recently, > and > > didn't see > > xxGENENAME or xxSYMBOL environments have any > > problem. So, I suspect the > > problem is specific to your input data. Could you > > please provide more > > details? e.g. myBaseType and maybe also a small > part > > of myBase > > Also, you may want to upgrade AnnBuilder to > 1.10.1. > > The UCSC Genome > > database updated their schema (one table) recently > > for human and mouse > > data, and AnnBuilder has been updated > > correspondingly. If you see > > problems with xxCHRLOC environment, please update > > your AnnBuilder. > > > > thanks > > > > nianhua > > > > Nianhua Li > > Computational Biology, PHS, FHCRC > > > > _______________________________________________ > > 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 > > > > _______________________________________________ > 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, Weijun, Sorry for the late reply. I was travelling yesterday... Please add one tempty column to your base file myBase, so it will look like: 10001_at\t\t10001 10002_at\t\t10002 10003_at\t\t10003 Here "\t" is the TAB key, not string "\t". This modification will solve your problem. And you should get environments like: xxACCNUM, xxGENENAME, xxSYMBOL, xxGO, xxOMIM, xxPMID, etc. All those information are obtained from Entrez Gene. The Entrez Gene data is parsed by one of the parsers in folder AnnBuilder/scripts (or AnnBuilder/inst/scripts in source). The input parameter "baseMapType" of ABPkgbuilder decides which parser to use. The parser for baseMapType "ll" is "llParser". The parser seems to assume that the baseFile has at least three columns (delimited by TAB), and the first three columns should probeset ID, GenBank accession numbers, and Entrez Gene ID. Because we only use "Entrez Gene ID" for the mapping, the 2nd column can be empty, but you have to have two TAB delimiters there. When baseFile has only two columns, the parser will do something else. I am not sure whether it is a feature or a bug. But I am hesitate to modify it cauz other packages may depend on it. If anyone is familiar with this part, I will appreciate if you could give some comments. Also, just FYI, even though many annotation packages in bioc were generated by ABPkgBuilder, none of them use "ll" as "baseMapType". So, we didn't realize this problem before. Thanks you for bring this up. We will either update the document or provide a patch in the near future. many thanks nianhua Nianhua Li computational biology, PHS, FHCRC
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Thank you so much, Nianhua, I think it works now. One more question, You suggested me to update AnnBuilder to the lastest version, 1.10.1, since The UCSC Genome database has updated. But I am not sure exactly how to do it. I tried to update AnnBuilder package with biocLite('AnnBuilder'), as well as using update.packages(repos=biocReposList()) following Seth??s suggestion, all I got is still the old version, AnnBuilder_1.10.0. Therefore, could you tell me how can I update to the lastest AnnBuilder version? This is my session info after update.packages(repos=biocReposList()) > sessionInfo() Version 2.3.1 (2006-06-01) powerpc-apple-darwin8.6.0 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: AnnBuilder RSQLite DBI annotate XML Biobase "1.10.0" "0.4-1" "0.1-10" "1.10.0" "0.99-7" "1.10.0" > I really appreciate your help! Weijun
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Sorry, the OS X version of AnnBuilder v1.10.2 is not available yet. We will try to get it ready as soon as possible. Alternatively, you can download the source from http://www.bioconductor.org/packages/bioc/1.8/html/AnnBuilder.html and install it yourself. The modification that matters to you is in AnnBuilder/R/GP.R . best nianhua Quoting Luo Weijun <luo_weijun at="" yahoo.com="">: > Thank you so much, Nianhua, > I think it works now. One more question, You suggested > me to update AnnBuilder to the lastest version, > 1.10.1, since The UCSC Genome > database has updated. But I am not sure exactly how to > do it. I tried to update AnnBuilder package with > biocLite('AnnBuilder'), as well as using > update.packages(repos=biocReposList()) following > Seth??s suggestion, all I got is still the old > version, AnnBuilder_1.10.0. Therefore, could you tell > me how can I update to the lastest AnnBuilder version? > > This is my session info after > update.packages(repos=biocReposList()) > > > sessionInfo() > Version 2.3.1 (2006-06-01) > powerpc-apple-darwin8.6.0 > > attached base packages: > [1] "tools" "methods" "stats" "graphics" > "grDevices" "utils" > [7] "datasets" "base" > > other attached packages: > AnnBuilder RSQLite DBI annotate XML > Biobase > "1.10.0" "0.4-1" "0.1-10" "1.10.0" "0.99-7" > "1.10.0" > > > I really appreciate your help! > Weijun > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com >
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Hello Nianhua, I installed the updated version of AnnBuilder successfully following your suggestion. The bad news is that I still don??t have the gene information, xxACCNUM, xxGENENAME, xxSYMBOL, xxGO, xxOMIM, xxPMID, etc, in my built annotation package, after I inserted one empty column between probe names and Entrez Gene ID columns in my base file. Here is what I got: > library(hs95av2Entrezg7) > hs95av2Entrezg7() Quality control information for hs95av2Entrezg7 Date built: Created: Thu Jul 13 12:25:38 2006 Number of probes: 8359 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: hs95av2Entrezg7ACCNUM found 0 of 8359 hs95av2Entrezg7CHRLOC found 8042 of 8359 hs95av2Entrezg7ENZYME found 1315 of 8359 hs95av2Entrezg7LOCUSID found 8292 of 8359 hs95av2Entrezg7PATH found 2785 of 8359 Mappings found for non-probe based rda files: hs95av2Entrezg7CHRLENGTHS found 25 hs95av2Entrezg7ENZYME2PROBE found 652 hs95av2Entrezg7ORGANISM found 1 hs95av2Entrezg7PATH2PROBE found 180 hs95av2Entrezg7PFAM found 6934 hs95av2Entrezg7PROSITE found 4941 >a=read.delim('/Users/luow/project/microarraydata/annotation/hs95av2En trezg7Base.txt',sep='\t', head=F) > head(a) V1 V2 V3 1 10001_at NA 10001 2 10002_at NA 10002 3 10003_at NA 10003 4 10004_at NA 10004 5 10005_at NA 10005 6 10006_at NA 10006 > Below is my sessionInfo when I build the annotation. Actually before I updated AnnBuilder, the same thing happened when I used a 3-column base file. It seems to me that to get those gene information data, our current llParser needs GenBank accession numbers in the 2nd column. But it doesn??t make too much sense to me, since to pull out gene information from NCBI Entrez Gene database, we just need any one of the commonly used gene IDs?? Please let me know what I can do about this. Thank you again for all your kind help. Weijun > sessionInfo() Version 2.3.1 (2006-06-01) powerpc-apple-darwin8.6.0 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: AnnBuilder RSQLite DBI annotate XML Biobase "1.10.2" "0.4-1" "0.1-10" "1.10.0" "0.99-7" "1.10.0" > --- nli at fhcrc.org wrote: > Sorry, the OS X version of AnnBuilder v1.10.2 is not > available yet. We will try > to get it ready as soon as possible. Alternatively, > you can download the source > from > http://www.bioconductor.org/packages/bioc/1.8/html/AnnBuilder.html > and > install it yourself. The modification that matters > to you is in > AnnBuilder/R/GP.R . > > best > > nianhua > > Quoting Luo Weijun <luo_weijun at="" yahoo.com="">: > > > Thank you so much, Nianhua, > > I think it works now. One more question, You > suggested > > me to update AnnBuilder to the lastest version, > > 1.10.1, since The UCSC Genome > > database has updated. But I am not sure exactly > how to > > do it. I tried to update AnnBuilder package with > > biocLite('AnnBuilder'), as well as using > > update.packages(repos=biocReposList()) following > > Seth??s suggestion, all I got is still the old > > version, AnnBuilder_1.10.0. Therefore, could you > tell > > me how can I update to the lastest AnnBuilder > version? > > > > This is my session info after > > update.packages(repos=biocReposList()) > > > > > sessionInfo() > > Version 2.3.1 (2006-06-01) > > powerpc-apple-darwin8.6.0 > > > > attached base packages: > > [1] "tools" "methods" "stats" "graphics" > > > "grDevices" "utils" > > [7] "datasets" "base" > > > > other attached packages: > > AnnBuilder RSQLite DBI annotate > XML > > Biobase > > "1.10.0" "0.4-1" "0.1-10" "1.10.0" > "0.99-7" > > "1.10.0" > > > > > I really appreciate your help! > > Weijun > > > > > > __________________________________________________ > > Do You Yahoo!? > protection around > > http://mail.yahoo.com > > > > > > >
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