Question: Error using yeastPkgBuilder (AnnBuilder package)
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gravatar for melany black
12.2 years ago by
melany black30
melany black30 wrote:
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ADD COMMENTlink modified 12.2 years ago by Marc Carlson7.2k • written 12.2 years ago by melany black30
Answer: Error using yeastPkgBuilder (AnnBuilder package)
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gravatar for melany black
12.2 years ago by
melany black30
melany black30 wrote:
(sorry for the html in the previous mail) Hi, I'm trying to build an annotation package for yeast chips using AnnBuilder. I was successful, but at the end, I got an error. Here's my code: > library("AnnBuilder") > read.table(file.path(.path.package("AnnBuilder"), "data", "yeastsgd"),sep = "\t", header = FALSE, as.is = TRUE)[1:5,] V1 V2 1 A_75_00001 S000005688 2 A_75_00002 S000005689 3 A_75_00003 S000005690 4 A_75_00004 S000005691 5 A_75_00005 S000005692 > myBase <- file.path(.path.package("AnnBuilder"), "data", "yeastsgd") > myDir <- tempdir() > yeastPkgBuilder(pkgName="yeastAgilent",pkgPath=myDir,base=myBase,versi on = "1.1.0",author = list(authors = "mel", maintainer ="mel.black at yahoo.fr"), fromWeb=TRUE) package directory structure initialized annotation data read complete 1:1 PROBE mappings complete 1:many PROBE mappings complete CHRLOC complete Error in l2e(dList, env) : require a list Warning messages: 1: Organism Saccharomyces cerevisiae is not supported by GoldenPath (GP). in: getUCSCUrl(organism) 2: no argument for max ; -Inf is returned in: max(i) The following files were created in "yeastAgilent\data" folder: yeastAgilentALIAS.rda yeastAgilentCHR.rda yeastAgilentCHRLOC.rda yeastAgilentDESCRIPTION.rda yeastAgilentGENENAME.rda yeastAgilentORF.rda yeastAgilentPMID.rda Hope someone could explain me where this error comes from, and how to fix it. > 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: GO AnnBuilder annotate XML Biobase "1.16.0" "1.14.0" "1.14.1" "1.9-0" "1.14.1" Mel.
ADD COMMENTlink written 12.2 years ago by melany black30
Answer: Error using yeastPkgBuilder (AnnBuilder package)
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gravatar for Marc Carlson
12.2 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
melany black wrote: > Hi, > > I'm trying to build an annotation package for yeast chips using AnnBuilder. > I was successful, but at the end, I got an error. > Here's my code: > > > library("AnnBuilder") > >> read.table(file.path(.path.package("AnnBuilder"), "data", "yeastsgd"),sep = "\t", header = FALSE, as.is = TRUE)[1:5,] >> > V1 V2 > 1 A_75_00001 S000005688 > 2 A_75_00002 S000005689 > 3 A_75_00003 S000005690 > 4 A_75_00004 S000005691 > 5 A_75_00005 S000005692 > > >> myBase <- file.path(.path.package("AnnBuilder"), "data", "yeastsgd") >> myDir <- tempdir() >> yeastPkgBuilder(pkgName="yeastAgilent",pkgPath=myDir,base=myBase,ve rsion = "1.1.0", >> > + author = list(authors = "mel", maintainer ="mel.black at yahoo.fr"), fromWeb=TRUE) > > package directory structure initialized > annotation data read complete > 1:1 PROBE mappings complete > 1:many PROBE mappings complete > CHRLOC complete > Error in l2e(dList, env) : require a list > Warning messages: > 1: Organism Saccharomyces cerevisiae is not supported by GoldenPath (GP). in: getUCSCUrl(organism) > 2: no argument for max ; -Inf is returned in: max(i) > > The following files were created in "yeastAgilent\data" folder: > yeastAgilentALIAS.rda > yeastAgilentCHR.rda > yeastAgilentCHRLOC.rda > yeastAgilentDESCRIPTION.rda > yeastAgilentGENENAME.rda > yeastAgilentORF.rda > yeastAgilentPMID.rda > > Hope someone could explain me where this error comes from, and how to fix it. > > > sessionInfo() > R version 2.5.1 (2007-06-27) > i386-pc-mingw32 > locale: > LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETAR Y=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: > GO AnnBuilder annotate XML Biobase > "1.16.0" "1.14.0" "1.14.1" "1.9-0" "1.14.1" > > > Mel. > > > --------------------------------- > > [[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 > > Hi Melany, After some testing I have discovered that the major source of your problem is that you are not using the correct kind of IDs. YeastPkgBuilder is older code and was apparently designed before SGD IDs saw wider usage. You will have better luck if you first convert to "ORF" style IDs. So in your case the 1st 5 rows of your base file should look more like: A_75_00001 YOR162C A_75_00002 YOR163W A_75_00003 YOR164C A_75_00004 YOR165W A_75_00005 YOR166C Instead of: A_75_00001 S000005688 A_75_00002 S000005689 A_75_00003 S000005690 A_75_00004 S000005691 A_75_00005 S000005692 Please rest assured that we are working towards getting rid of these kinds of problems in the future. Marc
ADD COMMENTlink written 12.2 years ago by Marc Carlson7.2k
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