Question: problem with GO annotation data
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gravatar for swang
13.2 years ago by
swang120
swang120 wrote:
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ADD COMMENTlink modified 13.2 years ago by Seth Falcon7.4k • written 13.2 years ago by swang120
Answer: problem with GO annotation data
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gravatar for Nianhua Li
13.2 years ago by
Nianhua Li870
Nianhua Li870 wrote:
Hi, Shiliang, You were right that AnnBuilder did have a bug. Thanks for the report! The bug is related to Weijun's question: http://thread.gmane.org/gmane.science.biology.informatics.conductor/92 27/focus=9232 When baseType is "ll", the baseFile can't be parsed correctly because some parsers assume Entrez Gene is at the 3rd column of the base file. Thanks for John's patch, AnnBuilder just quietly converts the base file into three columns when baseType is "ll". So, weijun's problem got solved. Unfortunately, the parser used for "go2probe" mapping assumes a two-column setting for baseType "ll", therefore can't work correctly with the patch. Now the problem has been solved. You can either get the up-to-date AnnBuilder (v 1.11.6) from svn or wait still Saturday noon to download it using biocLite or from website. You can also modify your local source AnnBuilder/R/ABPkgBuilder.R if you are in a hurry: =================================================================== --- ABPkgBuilder.R (v1.11.5 or before) +++ ABPkgBuilder.R (v1.11.6) # Map GO ids to probe ids that are directly associated with the GO ids mapGO2Probe <- function(eg, baseMapType){ - if(baseMapType == "ll"){ - parser(eg) <- file.path(.path.package("AnnBuilder"), - "scripts", "GO2ProbeParser4LL") - }else{ - parser(eg) <- file.path(.path.package("AnnBuilder"), + parser(eg) <- file.path(.path.package("AnnBuilder"), "scripts", "GO2ProbeParser") - } options(show.error.messages = FALSE) go2Probe <- try(parseData(eg, eg at go, ncol = 3)) options(show.error.messages = TRUE) ==================================================================== Also the probe number mismatch is because your base file has duplicated probeset identifiers. help it works this time :) nianhua
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ADD REPLYlink written 13.2 years ago by swang120
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Answer: problem with GO annotation data
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gravatar for Seth Falcon
13.2 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
John Zhang <jzhang at="" jimmy.harvard.edu=""> writes: >>Also, I found I cannot use some of function in AnnBuilder, I don't know why? >>I used it because I want to reproduce the result from AnnBuilder.pdf from >>the package review. it always give me error. > > It is a name space issue. Try AnnBuilder:::functionName To get going quickly, sure. But breaking namespace protection using ':::' is not, in general, a good idea. If there are functions that should be exported, let's export them. + seth
ADD COMMENTlink written 13.2 years ago by Seth Falcon7.4k
Answer: problem with GO annotation data
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gravatar for Seth Falcon
13.2 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
swang <swang2000 at="" gmail.com=""> writes: > Nianhua: > > Sorry to bother you again! I tried to fix my local AnnBuilder source > code as you said. But the problem is the code is not as you said I > pasted them underneath: how can I get it worked. At this point, you really need to take a moment and get aquainted with svn. The whole point of such tools is to help developers collaborate and to avoid confusion about which version of a file one is discussing/editing, etc. Pretty please have a look at svn and see if that resolved your source code confusion. + seth
ADD COMMENTlink written 13.2 years ago by Seth Falcon7.4k
Answer: problem with GO annotation data
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gravatar for John Zhang
13.2 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
>Also, I found I cannot use some of function in AnnBuilder, I don't know why? >I used it because I want to reproduce the result from AnnBuilder.pdf from >the package review. it always give me error. It is a name space issue. Try AnnBuilder:::functionName > >Best > >Shiliang > > > > >R : Copyright 2006, The R Foundation for Statistical Computing >Version 2.3.1 (2006-06-01) >ISBN 3-900051-07-0 > >R is free software and comes with ABSOLUTELY NO WARRANTY. >You are welcome to redistribute it under certain conditions. >Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > >R is a collaborative project with many contributors. >Type 'contributors()' for more information and >'citation()' on how to cite R or R packages in publications. > >Type 'demo()' for some demos, 'help()' for on-line help, or >'help.start()' for an HTML browser interface to help. >Type 'q()' to quit R. > >[Previously saved workspace restored] > >> library(AnnBUilder) >Error in library(AnnBUilder) : there is no package called 'AnnBUilder' >> library(AnnBuilder) >Loading required package: Biobase >Loading required package: tools > >Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details > on reading vignettes, see the openVignette help page. > >Loading required package: XML >Loading required package: annotate > >Attaching package: 'annotate' > > > The following object(s) are masked _by_ .GlobalEnv : > > getGO > >Loading required package: RSQLite >Loading required package: DBI >> writeAnnData2Pkg >Error: object "writeAnnData2Pkg" not found >> getChroLocation >Error: object "getChroLocation" not found >> > > > >On 7/27/06, Nianhua Li <nli at="" fhcrc.org=""> wrote: >> >> Hi, Shiliang, >> >> You were right that AnnBuilder did have a bug. Thanks for the report! >> >> The bug is related to Weijun's question: >> >> http://thread.gmane.org/gmane.science.biology.informatics.conductor/92 27/focus=9 232 >> When baseType is "ll", the baseFile can't be parsed correctly because >> some parsers assume Entrez Gene is at the 3rd column of the base file. >> Thanks for John's patch, AnnBuilder just quietly converts the base file >> into three columns when baseType is "ll". So, weijun's problem got >> solved. Unfortunately, the parser used for "go2probe" mapping assumes a >> two-column setting for baseType "ll", therefore can't work correctly >> with the patch. >> >> Now the problem has been solved. You can either get the up-to-date >> AnnBuilder (v 1.11.6) from svn or wait still Saturday noon to download >> it using biocLite or from website. You can also modify your local source >> AnnBuilder/R/ABPkgBuilder.R if you are in a hurry: >> =================================================================== >> --- ABPkgBuilder.R (v1.11.5 or before) >> +++ ABPkgBuilder.R (v1.11.6) >> >> # Map GO ids to probe ids that are directly associated with the GO ids >> mapGO2Probe <- function(eg, baseMapType){ >> - if(baseMapType == "ll"){ >> - parser(eg) <- file.path(.path.package("AnnBuilder"), >> - "scripts", "GO2ProbeParser4LL") >> - }else{ >> - parser(eg) <- file.path(.path.package("AnnBuilder"), >> + parser(eg) <- file.path(.path.package("AnnBuilder"), >> "scripts", "GO2ProbeParser") >> - } >> options(show.error.messages = FALSE) >> go2Probe <- try(parseData(eg, eg at go, ncol = 3)) >> options(show.error.messages = TRUE) >> ==================================================================== >> >> Also the probe number mismatch is because your base file has duplicated >> probeset identifiers. >> >> help it works this time :) >> >> nianhua >> >> > > [[alternative HTML version deleted]] > >_______________________________________________ >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
ADD COMMENTlink written 13.2 years ago by John Zhang2.9k
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ADD REPLYlink written 13.2 years ago by swang120
Hi, Shiliang, The date of your quality control data in your post is: Quality control information for Rosetta Date built: Created: Thu Jul 27 16:38:20 2006 It is the same as the date (of quality control data) on your post yesterday. This means you are using the old version of your data package. Could you double check that? The "symbol.C" may related to your sqlite installation... I am double checking the AnnBuilder package now, and will let you know if I find any problems. thanks nianhua
ADD REPLYlink written 13.2 years ago by Nianhua Li870
Hi, Shiliang, I test AnnBuilder 1.11.6 again by using the sample data in your post yesterday: ------------------------------------- 10024407494 11307 10024401025 11308 10024394441 11370 10024403966 11409 10024409675 11416 10024409230 11418 10024410196 11419 10024397993 11421 --------------------------------------- And this is the result: ---------------------------------------------------------------------- ------ Quality control information for mypkg Date built: Created: Fri Jul 28 12:45:18 2006 Number of probes: 8 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: mypkgACCNUM found 0 of 8 mypkgCHRLOC found 8 of 8 mypkgCHR found 8 of 8 mypkgENZYME found 3 of 8 mypkgGENENAME found 8 of 8 mypkgGO found 8 of 8 mypkgLOCUSID found 8 of 8 mypkgMAP found 8 of 8 mypkgPATH found 5 of 8 mypkgPMID found 8 of 8 mypkgREFSEQ found 8 of 8 mypkgSUMFUNC found 0 of 8 mypkgSYMBOL found 8 of 8 mypkgUNIGENE found 8 of 8 Mappings found for non-probe based rda files: mypkgCHRLENGTHS found 21 mypkgENZYME2PROBE found 3 mypkgGO2ALLPROBES found 182 mypkgGO2PROBE found 65 mypkgORGANISM found 1 mypkgPATH2PROBE found 8 mypkgPFAM found 7 mypkgPMID2PROBE found 178 mypkgPROSITE found 6 ---------------------------------------------------------------------- -- Seems the result is ok. So, please check your environment. And good luck! nianhua
ADD REPLYlink written 13.2 years ago by Nianhua Li870
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