An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20060727/ 517e592d/attachment.pl

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

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

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

>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