AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)
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Luo Weijun ★ 1.6k
@luo-weijun-1783
Last seen 9 months ago
United States
Hello all, I tried to build annotation with AnnBuilder package. The base file I used has probe names and mapped Entrez Gene IDs (human genes). Things worked fine, except some failed connection to KEGG database. And I got the final annotation package, and it works, that is really cool. However, I didn't see the gene information data, like "GENENAME", "SYMBOL" etc, though. And this information is important for a complete annotation of my customized microarray platform. I looked at annotation packages for affy chips, all have gene information data. However, the whole human genome annotation package, humanLLMappings, doesn't have it. And since these are also built with AnnBuilder, I think something stop working properly in my case and in humanLLMappings' case. I studied the source codes from AnnBuilder package, and narrowed the problem down to the corresponding part in getAnnData function, which is called in ABPkgBuilder function. Here is that code chunk I extraced: parser(srcObjs[["eg"]]) <- getBaseParsers("eginfo") geneinfo <- try(parseData(srcObjs[["eg"]], srcObjs[["eg"]]@info, ncol = 5, mergeKey = FALSE)) colnames(geneinfo) <- c("PROBE", "SYMBOL", "GENENAME", "CHR", "MAP") options(show.error.messages = TRUE) if (inherits(annotation, "try-error")) { stop(paste("Parsing Entrez Gene gene_info.gz failed because of:\n\n", annotation)) } if (nrow(geneinfo) > 0) annotation <- merge(annotation, geneinfo, by = "PROBE", all.x = TRUE) I am not sure what problem happens here, but there is no error message shown, and which means I did get something assigned to geneinfo, but geneinfo is not merge into annotation, very likely it has 0 rows. I am not sure I am correct here, but please let me know if you have any idea, and you know how to solve this problem. Thank you so much in advance. Here is the code I use to build my 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) print(date()) And my 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" Weijun
Microarray Annotation probe annotate affy AnnBuilder Microarray Annotation probe annotate • 1.7k views
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John Zhang ★ 2.9k
@john-zhang-6
Last seen 9.6 years ago
But what was your base map type (baseMapType = ?)? >X-Original-To: jzhang at jimmy.harvard.edu >Delivered-To: jzhang at jimmy.harvard.edu >DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:Cc:MIME-Version:Content- Type:Content- Transfer-Encoding; b=P1N/Dp4dpo+k/SKYAvznRmJqPOMk6UE6o6Txl319OQtLbcvooC7ztxQGQBKAKNCzwNqr uklPTCJ1q2 11Gfreycwn//EL4XRFBA+tI/xtE9kwGvq1L10gqj/KbrjFg4uR9n1OCvjuw9RP+6i08MH0 8zDXLE+6aX 0P1PP9NfWIFjs= ; >Date: Sun, 9 Jul 2006 18:46:26 -0700 (PDT) >From: Luo Weijun <luo_weijun at="" yahoo.com=""> >Subject: AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc) >To: bioconductor at stat.math.ethz.ch >Cc: jzhang at jimmy.harvard.edu >MIME-Version: 1.0 >Content-Transfer-Encoding: 8bit >X-PMX-Version: 5.2.0.266434, Antispam-Engine: 2.4.0.264935, Antispam- Data: 2006.7.9.183432 >X-PMX-Spam: Probability=7%, Report='__CP_URI_IN_BODY 0, __CT 0, __CTE 0, __CT_TEXT_PLAIN 0, __DOMAINKEYS_YAHOO 0, __HAS_MSGID 0, __MIME_TEXT_ONLY 0, __MIME_VERSION 0, __SANE_MSGID 0, __STOCK_CRUFT 0' > >Hello all, >I tried to build annotation with AnnBuilder package. >The base file I used has probe names and mapped Entrez >Gene IDs (human genes). Things worked fine, except >some failed connection to KEGG database. And I got the >final annotation package, and it works, that is really >cool. However, I didn't see the gene information data, >like "GENENAME", "SYMBOL" etc, though. And this >information is important for a complete annotation of >my customized microarray platform. >I looked at annotation packages for affy chips, all >have gene information data. However, the whole human >genome annotation package, humanLLMappings, doesn't >have it. And since these are also built with >AnnBuilder, I think something stop working properly in >my case and in humanLLMappings' case. >I studied the source codes from AnnBuilder package, >and narrowed the problem down to the corresponding >part in getAnnData function, which is called in >ABPkgBuilder function. Here is that code chunk I >extraced: > > parser(srcObjs[["eg"]]) <- >getBaseParsers("eginfo") > geneinfo <- try(parseData(srcObjs[["eg"]], >srcObjs[["eg"]]@info, > ncol = 5, mergeKey = FALSE)) > colnames(geneinfo) <- c("PROBE", "SYMBOL", >"GENENAME", "CHR", > "MAP") > options(show.error.messages = TRUE) > if (inherits(annotation, "try-error")) { > stop(paste("Parsing Entrez Gene gene_info.gz >failed because of:\n\n", > annotation)) > } > if (nrow(geneinfo) > 0) > annotation <- merge(annotation, geneinfo, by = >"PROBE", > all.x = TRUE) > >I am not sure what problem happens here, but there is >no error message shown, and which means I did get >something assigned to geneinfo, but geneinfo is not >merge into annotation, very likely it has 0 rows. >I am not sure I am correct here, but please let me >know if you have any idea, and you know how to solve >this problem. Thank you so much in advance. > >Here is the code I use to build my 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) >print(date()) > >And my 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" > > >Weijun > > >__________________________________________________ >Do You Yahoo!? >Tired of spam? Yahoo! Mail has the best spam protection around >http://mail.yahoo.com Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
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Seth Falcon ★ 7.4k
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Last seen 9.6 years ago
Hi Weijun, Luo Weijun <luo_weijun at="" yahoo.com=""> writes: > 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. You may need to give folks a bit more time to respond. Nianhua is on a business trip and probably won't have time to reply until late next week. > 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? You can get the update using biocLite: source("http://bioconductor.org/biocLite.R") biocLite("AnnBuilder") You can update all of your installed packages to their latest available versions like this: library("Biobase") update.packages(repos=biocReposList()) + seth
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John Zhang ★ 2.9k
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Last seen 9.6 years ago
>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: I have fixed the code. You may want to wait to use the new version off the developmental track. > >> 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/hs95av2E ntrezg7Bas e.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 >> > >> >> >> >> >> > >_______________________________________________ >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 Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
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Thank you, John. Shall I use 2-column or 3-column base file for the new version of AnnBuilder? And the new version number will be 1.10.2 or 1.10.3? I have already seen an OS X binary version shown up in AnnBuilder website, http://www.bioconductor.org/packages/bioc/1.8/html/AnnBuilder.html, I am not sure whether that's the new version. Weijun --- John Zhang <jzhang at="" jimmy.harvard.edu=""> wrote: > > >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: > > I have fixed the code. You may want to wait to use > the new version off the > developmental track. > > > > > > >> 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/hs95av2E ntrezg7Bas > e.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 > >> > > >> > >> > >> > >> > >> > > > >_______________________________________________ > >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 > > Jianhua Zhang > Department of Medical Oncology > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 > >
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John Zhang ★ 2.9k
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Last seen 9.6 years ago
>Thank you, John. Shall I use 2-column or 3-column base Two columns. >file for the new version of AnnBuilder? And the new The version I checked in is 1.11.4. I am not sure when the new version will be pushed. Nianhua knows better. >version number will be 1.10.2 or 1.10.3? I have >already seen an OS X binary version shown up in >AnnBuilder website, >http://www.bioconductor.org/packages/bioc/1.8/html/AnnBuilder.html, > I am not sure whether that's the new version. >Weijun > >--- John Zhang <jzhang at="" jimmy.harvard.edu=""> wrote: > >> >> >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: >> >> I have fixed the code. You may want to wait to use >> the new version off the >> developmental track. >> >> >> >> > >> >> 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/hs95av2 Entrezg7Ba s >> e.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 >> >> > >> >> >> >> >> >> >> >> >> >> >> > >> >_______________________________________________ >> >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 >> >> Jianhua Zhang >> Department of Medical Oncology >> Dana-Farber Cancer Institute >> 44 Binney Street >> Boston, MA 02115-6084 >> >> > > >__________________________________________________ >Do You Yahoo!? >Tired of spam? Yahoo! Mail has the best spam protection around >http://mail.yahoo.com Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
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Hi, It seems we have some problems here. Let me clarify things first: 1. There are two svn source repositories: the bioconductor 1.8 release repository where AnnBuilder 1.10.x belong to and the devel repository where AnnBuilder 1.11.x belong to. John fixed the problem of AnnBuilder at the devel repository today and the latest version is 1.11.4. You can get the code from our svn repository at https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnBuilder now, or you can get it from http://www.bioconductor.org/packages/1.9/bioc/html/AnnBuilder.html TOMORROW. The corresponding OS X binary will be ready after a week. 2. The packages in devel repository (including AnnBuilder 1.11.x) are for R 2.4.x. Therefore, they may not be backward compatiable with R 2.3.x. Please give it a try. I am not able to test it in my current setting. Sorry. 3. I thought AnnBuilder 1.10.x should work the same as 1.11.x, so I used 1.11.x for testing but referred to 1.10.x in my previous replies. But I was wrong, sorry. I tested both AnnBuilder 1.11.2 (3 column baseFile) and AnnBuilder 1.11.4 by using your exact baseFile, and both worked fine. I test AnnBuilder 1.10.x just now, but it didn't work. I need more time to look into it. I will update you later... Please try either AnnBuiler 1.11.2 or 1.11.4 for now. Sorry for the inconvenience. nianhua Quoting John Zhang <jzhang at="" jimmy.harvard.edu="">: > > >Thank you, John. Shall I use 2-column or 3-column base > > Two columns. > > >file for the new version of AnnBuilder? And the new > > The version I checked in is 1.11.4. I am not sure when the new version will > be > pushed. Nianhua knows better. > > > >version number will be 1.10.2 or 1.10.3? I have > >already seen an OS X binary version shown up in > >AnnBuilder website, > >http://www.bioconductor.org/packages/bioc/1.8/html/AnnBuilder.html, > > I am not sure whether that's the new version. > >Weijun > > > >--- John Zhang <jzhang at="" jimmy.harvard.edu=""> wrote: > > > >> > >> >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: > >> > >> I have fixed the code. You may want to wait to use > >> the new version off the > >> developmental track. > >> > >> > >> > >> > > >> >> 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/hs95av2 Entrezg7Ba > s > >> e.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 > >> >> > > >> >> > >> >> > >> >> > >> >> > >> >> > >> > > >> >_______________________________________________ > >> >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 > >> > >> Jianhua Zhang > >> Department of Medical Oncology > >> Dana-Farber Cancer Institute > >> 44 Binney Street > >> Boston, MA 02115-6084 > >> > >> > > > > > >__________________________________________________ > >Do You Yahoo!? > >Tired of spam? Yahoo! Mail has the best spam protection around > >http://mail.yahoo.com > > Jianhua Zhang > Department of Medical Oncology > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 > >
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Thanks a lot, I will wait till tomorrow to get the source code from bioconductor website, since the website at https://hedgehog.fhcrc.org/ needs account/password. And I agree there may be some backward compatibility issues between AnnBuilder 1.11.x and R 2.3.x. (I will try it out tomorrow.) In that case, I can only use AnnBuilder 1.10.x currently and in the near future, since R 2.4.x is not released yet. Therefore, I am looking forward to your results in checking AnnBuilder 1.10.x. Please keep me posted. Thanks. Weijun --- nli at fhcrc.org wrote: > Hi, > > It seems we have some problems here. Let me clarify > things first: > > 1. There are two svn source repositories: the > bioconductor 1.8 release > repository where AnnBuilder 1.10.x belong to and the > devel repository where > AnnBuilder 1.11.x belong to. John fixed the problem > of AnnBuilder at the devel > repository today and the latest version is 1.11.4. > You can get the code from > our svn repository at > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnBuilder > now, or > you can get it from > http://www.bioconductor.org/packages/1.9/bioc/html/AnnBuilder.html > TOMORROW. > The corresponding OS X binary will be ready after a > week. > > 2. The packages in devel repository (including > AnnBuilder 1.11.x) are for R > 2.4.x. Therefore, they may not be backward > compatiable with R 2.3.x. Please give > it a try. I am not able to test it in my current > setting. Sorry. > > 3. I thought AnnBuilder 1.10.x should work the same > as 1.11.x, so I used 1.11.x > for testing but referred to 1.10.x in my previous > replies. But I was wrong, > sorry. I tested both AnnBuilder 1.11.2 (3 column > baseFile) and AnnBuilder > 1.11.4 by using your exact baseFile, and both worked > fine. I test AnnBuilder > 1.10.x just now, but it didn't work. I need more > time to look into it. > > I will update you later... Please try either > AnnBuiler 1.11.2 or 1.11.4 for now. > Sorry for the inconvenience. > > nianhua > > > > Quoting John Zhang <jzhang at="" jimmy.harvard.edu="">: > > > > > >Thank you, John. Shall I use 2-column or 3-column > base > > > > Two columns. > > > > >file for the new version of AnnBuilder? And the > new > > > > The version I checked in is 1.11.4. I am not sure > when the new version will > > be > > pushed. Nianhua knows better. > > > > > > >version number will be 1.10.2 or 1.10.3? I have > > >already seen an OS X binary version shown up in > > >AnnBuilder website, > > > >http://www.bioconductor.org/packages/bioc/1.8/html/AnnBuilder.html, > > > I am not sure whether that's the new version. > > >Weijun > > > > > >--- John Zhang <jzhang at="" jimmy.harvard.edu=""> wrote: > > > > > >> > > >> >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: > > >> > > >> I have fixed the code. You may want to wait to > use > > >> the new version off the > > >> developmental track. > > >> > > >> > > >> > > >> > > > >> >> 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/hs95av2 Entrezg7Ba > > s > > >> e.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 > > >> >> > === message truncated ===
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Hi, weijun, Now you can download either AnnBuilder 1.11.4 from http://www.bioconductor.org/packages/1.9/bioc/html/AnnBuilder.html or AnnBuilder 1.10.4 from http://www.bioconductor.org/packages/1.8/bioc/html/AnnBuilder.html . Both have included John Zhang's patch, therefore should work for your case. thanks and good luck nianhua Quoting Luo Weijun <luo_weijun at="" yahoo.com="">: > Thanks a lot, > I will wait till tomorrow to get the source code from > bioconductor website, since the website at > https://hedgehog.fhcrc.org/ needs account/password. > And I agree there may be some backward compatibility > issues between AnnBuilder 1.11.x and R 2.3.x. (I will > try it out tomorrow.) In that case, I can only use > AnnBuilder 1.10.x currently and in the near future, > since R 2.4.x is not released yet. Therefore, I am > looking forward to your results in checking AnnBuilder > 1.10.x. Please keep me posted. Thanks. > Weijun
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Hello, Nianhua, I downloaded 1.11.4. And it works well under R 2.3.1, no compatibility issue. More important, I got the relevant gene information data I need. Finally it works! I have to say that I really appreciate you guys' work to make and improve this nice package. BTW, one more question, not urgent though, can I use Refseq ID as my base file mapping currently, or will this be considered in the future? Weijun --- nli at fhcrc.org wrote: > Hi, weijun, > > Now you can download either AnnBuilder 1.11.4 from > http://www.bioconductor.org/packages/1.9/bioc/html/AnnBuilder.html > or > AnnBuilder 1.10.4 from > http://www.bioconductor.org/packages/1.8/bioc/html/AnnBuilder.html > . Both have > included John Zhang's patch, therefore should work > for your case. > > thanks and good luck > > nianhua > > Quoting Luo Weijun <luo_weijun at="" yahoo.com="">: > > > Thanks a lot, > > I will wait till tomorrow to get the source code > from > > bioconductor website, since the website at > > https://hedgehog.fhcrc.org/ needs > account/password. > > And I agree there may be some backward > compatibility > > issues between AnnBuilder 1.11.x and R 2.3.x. (I > will > > try it out tomorrow.) In that case, I can only use > > AnnBuilder 1.10.x currently and in the near > future, > > since R 2.4.x is not released yet. Therefore, I am > > looking forward to your results in checking > AnnBuilder > > 1.10.x. Please keep me posted. Thanks. > > Weijun > > >
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John Zhang ★ 2.9k
@john-zhang-6
Last seen 9.6 years ago
>BTW, one more question, not urgent though, can I use >Refseq ID as my base file mapping currently, or will >this be considered in the future? Yes, just set baseMapType = "refseq" or "gbNRef". >Weijun > >--- nli at fhcrc.org wrote: > >> Hi, weijun, >> >> Now you can download either AnnBuilder 1.11.4 from >> >http://www.bioconductor.org/packages/1.9/bioc/html/AnnBuilder.html >> or >> AnnBuilder 1.10.4 from >> >http://www.bioconductor.org/packages/1.8/bioc/html/AnnBuilder.html >> . Both have >> included John Zhang's patch, therefore should work >> for your case. >> >> thanks and good luck >> >> nianhua >> >> Quoting Luo Weijun <luo_weijun at="" yahoo.com="">: >> >> > Thanks a lot, >> > I will wait till tomorrow to get the source code >> from >> > bioconductor website, since the website at >> > https://hedgehog.fhcrc.org/ needs >> account/password. >> > And I agree there may be some backward >> compatibility >> > issues between AnnBuilder 1.11.x and R 2.3.x. (I >> will >> > try it out tomorrow.) In that case, I can only use >> > AnnBuilder 1.10.x currently and in the near >> future, >> > since R 2.4.x is not released yet. Therefore, I am >> > looking forward to your results in checking >> AnnBuilder >> > 1.10.x. Please keep me posted. Thanks. >> > Weijun >> >> >> > >_______________________________________________ >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 Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
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