myEGs has length of 400 and all are in MyGeneUniverse, checked with setdiff. at hospital with mother having surgery today, so will post reproducible example when I can. assume that myEGs should be lengthy, not sure how to post this, hence the reason I did not post already. suggestions? thanks Mark ------------------------------------------------------------ Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** On Thu, Oct 23, 2008 at 12:52 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Hi Mark, > > From that output it looks like your package was made successfully. I > suspect that if you show us an example of what you were doing that we > might find the trouble in there. > > Marc > > > > > Mark Kimpel wrote: >>> ragene10stv1() >>> >> Quality control information for ragene10stv1: >> >> >> This package has the following mappings: >> >> ragene10stv1ACCNUM has 0 mapped keys (of 29214 keys) >> ragene10stv1ALIAS2PROBE has 31410 mapped keys (of 31410 keys) >> ragene10stv1CHR has 20998 mapped keys (of 29214 keys) >> ragene10stv1CHRLENGTHS has 23 mapped keys (of 23 keys) >> ragene10stv1CHRLOC has 13092 mapped keys (of 29214 keys) >> ragene10stv1CHRLOCEND has 13092 mapped keys (of 29214 keys) >> ragene10stv1ENSEMBL has 15812 mapped keys (of 29214 keys) >> ragene10stv1ENSEMBL2PROBE has 14570 mapped keys (of 14570 keys) >> ragene10stv1ENTREZID has 21170 mapped keys (of 29214 keys) >> ragene10stv1ENZYME has 1586 mapped keys (of 29214 keys) >> ragene10stv1ENZYME2PROBE has 705 mapped keys (of 705 keys) >> ragene10stv1GENENAME has 21170 mapped keys (of 29214 keys) >> ragene10stv1GO has 13813 mapped keys (of 29214 keys) >> ragene10stv1GO2ALLPROBES has 9850 mapped keys (of 9850 keys) >> ragene10stv1GO2PROBE has 7430 mapped keys (of 7430 keys) >> ragene10stv1MAP has 20351 mapped keys (of 29214 keys) >> ragene10stv1PATH has 4357 mapped keys (of 29214 keys) >> ragene10stv1PATH2PROBE has 206 mapped keys (of 206 keys) >> ragene10stv1PFAM has 17187 mapped keys (of 29214 keys) >> ragene10stv1PMID has 12198 mapped keys (of 29214 keys) >> ragene10stv1PMID2PROBE has 36641 mapped keys (of 36641 keys) >> ragene10stv1PROSITE has 17187 mapped keys (of 29214 keys) >> ragene10stv1REFSEQ has 18683 mapped keys (of 29214 keys) >> ragene10stv1SYMBOL has 21170 mapped keys (of 29214 keys) >> ragene10stv1UNIGENE has 17585 mapped keys (of 29214 keys) >> ragene10stv1UNIPROT has 9826 mapped keys (of 29214 keys) >> >> >> Additional Information about this package: >> >> DB schema: RATCHIP_DB >> DB schema version: 1.0 >> Organism: Rattus norvegicus >> Date for NCBI data: 2008-Sep2 >> Date for GO data: 200808 >> Date for KEGG data: 2008-Sep2 >> Date for Golden Path data: 2006-Jun20 >> Date for IPI data: 2008-Sep02 >> Date for Ensembl data: 2008-Jul23 >> >>> sessionInfo() >>> >> R version 2.8.0 (2008-10-20) >> x86_64-unknown-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=C >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] ragene10stv1.db_1.0.0 RSQLite_0.7-0 DBI_0.2-4 >> [4] AnnotationDbi_1.4.0 Biobase_2.2.0 graph_1.20.0 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.11 >> >> ------------------------------------------------------------ >> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >> Indiana University School of Medicine >> >> 15032 Hunter Court, Westfield, IN 46074 >> >> (317) 490-5129 Work, & Mobile & VoiceMail >> (317) 399-1219 Home >> Skype: mkimpel >> >> "The real problem is not whether machines think but whether men do." >> -- B. F. Skinner >> ****************************************************************** >> >> >> >> On Wed, Oct 22, 2008 at 7:41 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: >> >>> Hi Mark, >>> >>> If the package you built and installed were called "MarkPackage.db", >>> then what would be the output of "MarkPackage()" (right after you loaded >>> it)? Also, what is the output of sessionInfo()? >>> >>> Marc >>> >>> >>> >>> >>> Mark Kimpel wrote: >>> >>>> Today I believe I successfuly built a annotation package for my Affy >>>> Rat Gene ST data using annotationDbi, at least I got no errors during >>>> the build and it loads properly. I get the following error output, >>>> however, when I try to run hyperGTest, package Category, on a vector >>>> of Entrez Gene IDs and a vector of the gene universe of the chip. I >>>> suspect I did something wrong when building the annotation package, >>>> but I have no clue what that could be. I've used this same code with >>>> chipsets whose annotation packages are built by the BioConductor team >>>> without issue. >>>> >>>> >>>> >>>>> params <- new("GOHyperGParams", geneIds = myEGs, >>>>> >>>>> >>>> + universeGeneIds = myGeneUniverse, >>>> + annotation = annotation(AOP$eSet), >>>> + ontology = "BP", pvalueCutoff = 0.05, conditional >>>> = TRUE, testDirection = "over") >>>> >>>> >>>>> params >>>>> >>>>> >>>> A GOHyperGParams instance >>>> category: GO >>>> annotation: ragene10stv1 >>>> >>>> >>>>> hyperGTest(params) >>>>> >>>>> >>>> Error in getUniverseHelper(probes, datPkg, entrezIds) : >>>> No Entrez Gene ids left in universe >>>> >>>> Enter a frame number, or 0 to exit >>>> >>>> 1: hyperGTest(params) >>>> 2: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase", "hyperGT >>>> 3: is(object, Cl) >>>> 4: is(object, Cl) >>>> 5: universeBuilder(p) >>>> 6: universeBuilder(p) >>>> 7: getUniverseViaGo(p) >>>> 8: getUniverseHelper(probes, datPkg, entrezIds) >>>> >>>> Selection: 8 >>>> Called from: eval(expr, envir, enclos) >>>> Browse[1]> ls() >>>> [1] "datPkg" "entrezIds" "probes" "univ" >>>> Browse[1]> datPkg >>>> An object of class "ArabadopsisDatPkg" >>>> Slot "name": >>>> [1] "ragene10stv1" >>>> >>>> Browse[1]> entrezIds[1:5] >>>> [1] "65049" "60444" "313914" "140941" "306868" >>>> Browse[1]> probes[1:5] >>>> [1] "10701636" "10701643" "10701654" "10701663" "10701679" >>>> Browse[1]> univ >>>> character(0) >>>> Browse[1]> >>>> >>>> ------------------------------------------------------------ >>>> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >>>> Indiana University School of Medicine >>>> >>>> 15032 Hunter Court, Westfield, IN 46074 >>>> >>>> (317) 490-5129 Work, & Mobile & VoiceMail >>>> (317) 399-1219 Home >>>> Skype: mkimpel >>>> >>>> "The real problem is not whether machines think but whether men do." >>>> -- B. F. Skinner >>>> >>>> _______________________________________________ >>>> 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 >>>> >>>> >>>> >>> >> >> > >