Error using yeastPkgBuilder (AnnBuilder package)
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melany black ▴ 30
@melany-black-2333
Last seen 10.3 years ago
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melany black ▴ 30
@melany-black-2333
Last seen 10.3 years ago
(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.
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 8.4 years ago
United States
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
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