Question: AnnBuilder questions
0
gravatar for melany black
12.1 years ago by
melany black30
melany black30 wrote:
Dear all, I tried to build an annotation package using AnnBuilder and YeastPkgBuilder function. I think I'm close to the end now, but I steel have some errors I don't really understand... Here's the code I used: > library("AnnBuilder") > read.table(file.path(.path.package("AnnBuilder"), "data", "sgdid"),sep = "\t", header = FALSE, as.is = TRUE)[1:5,] V1 V2 1 A_75_P0000001 TEL01L 2 A_75_P0000002 YAL067W-A 3 A_75_P0000003 YAL067C 4 A_75_P0000004 YAL067C 5 A_75_P0000005 YAL067C > myBase <- file.path(.path.package("AnnBuilder"), "data", "sgdid") >myDir <- tempdir() >yeastPkgBuilder(pkgName="yeastAgilent",pkgPath=myDir,base=myBase,vers ion = "1.1.0",author = list(authors = "Mel", maintainer ="Mel <melany.black at="" yahoo.fr="">"),fromWeb=TRUE) I got the final annotation package, install it to R using: rcmd build yeastAgilent rcmd build --binary yeastAgilent I tried to check the library, everything worked well except the following error : Problem number 1 : 'yeastAgilentLOCUSID' is deprecated rather use 'yeastAgilentENTREZID' see help("Deprecated") In fact help("Deprecated") didn't help me at all! Here's what my package looks like : > library("yeastAgilent") > yeastAgilent() Quality control information for yeastAgilent Date built: Created: Tue Aug 21 18:50:18 2007 Number of probes: 41419 Probe number missmatch: yeastAgilentALIAS; yeastAgilentCHR; yeastAgilentCHRLOC; yeastAgilentDESCRIPTION; yeastAgilentENZYME; yeastAgilentGENENAME; yeastAgilentGO; yeastAgilentORF; yeastAgilentPATH; yeastAgilentPMID Probe missmatch: None Mappings found for probe based rda files: yeastAgilentALIAS found 1800 of 41419 yeastAgilentCHR found 5653 of 41419 yeastAgilentCHRLOC found 4968 of 41419 yeastAgilentDESCRIPTION found 5653 of 41419 yeastAgilentENZYME found 814 of 41419 yeastAgilentGENENAME found 4634 of 41419 yeastAgilentGO found 5653 of 41419 yeastAgilentORF found 6934 of 41419 yeastAgilentPATH found 1190 of 41419 yeastAgilentPMID found 5560 of 41419 Mappings found for non-probe based rda files: yeastAgilentCHRLENGTHS found 17 yeastAgilentENZYME2PROBE found 475 yeastAgilentGO2ALLPROBES found 4404 yeastAgilentGO2PROBE found 2991 yeastAgilentORGANISM found 1 yeastAgilentPATH2PROBE found 99 yeastAgilentPMID2PROBE found 42190 - Problem number 2 : the number of probe should be 41418 and not 41419 (I checked my base file, it has 41418 lines) - Problem number 3 : very few probes have been annotated (1800 out of 41419 I guess) for example if I do: >getinf=function(g,flds=c("ALIAS","CHR","CHRLOC")){ > sapply(flds,function(x) lookUp(g, "yeastAgilent", x)) > } > getinf("A_75_P0006546") $ALIAS.A_75_P0006546 [1] NA $CHR.A_75_P0006546 [1] NA $CHRLOC.A_75_P0006546 [1] NA I just get a bunch of "NA"s, except for a very few number of probes. - Problem number 4 : YeastPkgBuilder doesn't create "yeastAgilentSYMBOL". It seems like this is always the case with this function. How can I overcome this? Because if I want to plot my probes on the chromosome using geneplotter, I get an error: > library("geneplotter") > chrLoc=buildChromLocation("yeastAgilent") Error in get(x, envir, mode, inherits) : "yeastAgilentSYMBOL" not found That's a real problem, because quite all the purpose of creating an annotation package was for using geneplotter. Here's my sessionInfo: > sessionInfo() R version 2.5.1 (2007-06-27) i386-pc-mingw32 locale: LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY= French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: YEAST GO AnnBuilder XML hgu95av2 geneplotter lattice annotate Biobase yeastAgilent "1.16.0" "1.16.0" "1.14.0" "1.9-0" "1.16.0" "1.14.0" "0.16-3" "1.14.1" "1.14.1" "1.1.0" Thanks for any comment. Mel.
ADD COMMENTlink modified 12.1 years ago by Marc Carlson7.2k • written 12.1 years ago by melany black30
Answer: AnnBuilder questions
0
gravatar for John Zhang
12.1 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
> >I tried to check the library, everything worked well >except the following error : > >Problem number 1 : > >'yeastAgilentLOCUSID' is deprecated >rather use 'yeastAgilentENTREZID' >see help("Deprecated") This applies to packages containing an Entrez gene id environment (named XXXENTREZID now but used to XXXLOCUSID). Since the yeast annotation pacakge does not have Entrez Gene id, you may just ignor the warning. > >In fact help("Deprecated") didn't help me at all! > > >Here's what my package looks like : > >> library("yeastAgilent") >> yeastAgilent() > > >Quality control information for yeastAgilent >Date built: Created: Tue Aug 21 18:50:18 2007 > >Number of probes: 41419 >Probe number missmatch: yeastAgilentALIAS; >yeastAgilentCHR; yeastAgilentCHRLOC; >yeastAgilentDESCRIPTION; yeastAgilentENZYME; >yeastAgilentGENENAME; yeastAgilentGO; yeastAgilentORF; >yeastAgilentPATH; yeastAgilentPMID >Probe missmatch: None >Mappings found for probe based rda files: > yeastAgilentALIAS found 1800 of 41419 > yeastAgilentCHR found 5653 of 41419 > yeastAgilentCHRLOC found 4968 of 41419 > yeastAgilentDESCRIPTION found 5653 of 41419 > yeastAgilentENZYME found 814 of 41419 > yeastAgilentGENENAME found 4634 of 41419 > yeastAgilentGO found 5653 of 41419 > yeastAgilentORF found 6934 of 41419 > yeastAgilentPATH found 1190 of 41419 > yeastAgilentPMID found 5560 of 41419 >Mappings found for non-probe based rda files: > yeastAgilentCHRLENGTHS found 17 > yeastAgilentENZYME2PROBE found 475 > yeastAgilentGO2ALLPROBES found 4404 > yeastAgilentGO2PROBE found 2991 > yeastAgilentORGANISM found 1 > yeastAgilentPATH2PROBE found 99 > yeastAgilentPMID2PROBE found 42190 > > >- Problem number 2 : the number of probe should be >41418 and not 41419 (I checked my base file, it has >41418 lines) > >- Problem number 3 : very few probes have been >annotated (1800 out of 41419 I guess) >for example if I do: >>getinf=function(g,flds=c("ALIAS","CHR","CHRLOC")){ >> sapply(flds,function(x) lookUp(g, "yeastAgilent", >x)) >> } >> getinf("A_75_P0006546") >$ALIAS.A_75_P0006546 >[1] NA > >$CHR.A_75_P0006546 >[1] NA > >$CHRLOC.A_75_P0006546 >[1] NA > >I just get a bunch of "NA"s, except for a very few >number of probes. > >- Problem number 4 : YeastPkgBuilder doesn't create >"yeastAgilentSYMBOL". It seems like this is always the >case with this function. >How can I overcome this? Because if I want to plot my >probes on the chromosome using geneplotter, I get an >error: > >> library("geneplotter") >> chrLoc=buildChromLocation("yeastAgilent") >Error in get(x, envir, mode, inherits) : >"yeastAgilentSYMBOL" not found >That's a real problem, because quite all the purpose >of creating an annotation package was for using >geneplotter. > >Here's my sessionInfo: > >> sessionInfo() >R version 2.5.1 (2007-06-27) >i386-pc-mingw32 > >locale: >LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY =French_Fr ance.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 > >attached base packages: >[1] "tools" "stats" "graphics" "grDevices" >"utils" "datasets" "methods" "base" > >other attached packages: > YEAST GO AnnBuilder XML > hgu95av2 geneplotter lattice annotate >Biobase yeastAgilent > "1.16.0" "1.16.0" "1.14.0" "1.9-0" > "1.16.0" "1.14.0" "0.16-3" "1.14.1" >"1.14.1" "1.1.0" > > >Thanks for any comment. > >Mel. > >_______________________________________________ >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 12.1 years ago by John Zhang2.9k
Answer: AnnBuilder questions
0
gravatar for Marc Carlson
12.1 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
melany black wrote: > > - Problem number 4 : YeastPkgBuilder doesn't create > "yeastAgilentSYMBOL". It seems like this is always the > case with this function. > How can I overcome this? Because if I want to plot my > probes on the chromosome using geneplotter, I get an > error: > > >> library("geneplotter") >> chrLoc=buildChromLocation("yeastAgilent") >> > Error in get(x, envir, mode, inherits) : > "yeastAgilentSYMBOL" not found > That's a real problem, because quite all the purpose > of creating an annotation package was for using > geneplotter. > > > So I fear that you might be out of luck for this purpose. It does not appear that the buildChromLocation() works with any of the yeast packages to date. This is because these packages do not have a <pkgname>SYMBOL map in them. We are working on better (less limited) packages for the future, though. I am preparing about 80 of them as we speak. Marc
ADD COMMENTlink written 12.1 years ago by Marc Carlson7.2k
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