I am using annaffy to annotate some rat data. When using the aafFunction in affaffy, all of the objects returned were "character(0)". I then tried the function using the example code from the help page. I was surprised to get the same result. Is there a problem here? Session info, example code, and results below. Thanks. Mark sessionInfo: R version 2.2.0, 2005-10-06, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" other attached packages: hgu95av2 annotate rat2302 reposTools affy annaffy KEGG GO Biobase RWinEdt "1.10.0" "1.8.0" "1.8.5" "1.8.0" "1.8.1" "1.2.0" "1.8.1" "1.6.5" "1.8.0" "1.7-3" Example code used: if (require(hgu95av2)) { data(aafExpr) probes <- geneNames(aafExpr) functions <- aafFunction(probes, "hgu95av2") show(functions[6:10]) } Results: An object of class "aafList" [[1]] An object of class "aafFunction" character(0) [[2]] An object of class "aafFunction" character(0) [[3]] An object of class "aafFunction" character(0) [[4]] An object of class "aafFunction" character(0) [[5]] An object of class "aafFunction" character(0) Mark W. Kimpel MD Official Business Address: Department of Psychiatry Indiana University School of Medicine Biotechnology, Research, & Training Center 1345 W. 16th Street Indianapolis, IN 46202

>I am using annaffy to annotate some rat data. When using the aafFunction >in affaffy, all of the objects returned were "character(0)". I then >tried the function using the example code from the help page. I was >surprised to get the same result. Is there a problem here? Session info, >example code, and results below. Thanks. Mark Yes, there is a problem but not on your side. The function tried to access the SUMFUNC environment of the annotation package. This element used to be available from LocusLink but we have not found the replacement yet after switching to Entrez Gene. That is why you did get anything useful. > >sessionInfo: > >R version 2.2.0, 2005-10-06, i386-pc-mingw32 > >attached base packages: >[1] "tools" "methods" "stats" "graphics" "grDevices" "utils" >"datasets" "base" > >other attached packages: > hgu95av2 annotate rat2302 reposTools affy annaffy >KEGG GO Biobase RWinEdt > "1.10.0" "1.8.0" "1.8.5" "1.8.0" "1.8.1" "1.2.0" >"1.8.1" "1.6.5" "1.8.0" "1.7-3" > >Example code used: > >if (require(hgu95av2)) { > data(aafExpr) > probes <- geneNames(aafExpr) > functions <- aafFunction(probes, "hgu95av2") > show(functions[6:10]) > } > >Results: > >An object of class "aafList" >[[1]] >An object of class "aafFunction" >character(0) > >[[2]] >An object of class "aafFunction" >character(0) > >[[3]] >An object of class "aafFunction" >character(0) > >[[4]] >An object of class "aafFunction" >character(0) > >[[5]] >An object of class "aafFunction" >character(0) > >Mark W. Kimpel MD > > > >Official Business Address: > > > >Department of Psychiatry > >Indiana University School of Medicine > >Biotechnology, Research, & Training Center > >1345 W. 16th Street > >Indianapolis, IN 46202 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

Kimpel, Mark William wrote: > I am using annaffy to annotate some rat data. When using the aafFunction > in affaffy, all of the objects returned were "character(0)". I then > tried the function using the example code from the help page. I was > surprised to get the same result. Is there a problem here? Session info, > example code, and results below. Thanks. Mark Looks like you are getting what you should be. From ?aafFunction Value: An 'aafList' of 'aafFunction' objects. NA values are returned as empty objects. > hgu95av2() Quality control information for hgu95av2 Date built: Created: Tue Aug 30 19:13:25 2005 Number of probes: 12625 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: hgu95av2ACCNUM found 12625 of 12625 hgu95av2CHRLOC found 11764 of 12625 hgu95av2CHR found 12266 of 12625 hgu95av2ENZYME found 1895 of 12625 hgu95av2GENENAME found 11506 of 12625 hgu95av2GO found 11319 of 12625 hgu95av2LOCUSID found 12337 of 12625 hgu95av2MAP found 12224 of 12625 hgu95av2OMIM found 9972 of 12625 hgu95av2PATH found 3843 of 12625 hgu95av2PMID found 12203 of 12625 hgu95av2REFSEQ found 12114 of 12625 hgu95av2SUMFUNC found 0 of 12625 hgu95av2SYMBOL found 12280 of 12625 hgu95av2UNIGENE found 12225 of 12625 Mappings found for non-probe based rda files: hgu95av2CHRLENGTHS found 25 hgu95av2ENZYME2PROBE found 632 hgu95av2GO2ALLPROBES found 5574 hgu95av2GO2PROBE found 4011 hgu95av2ORGANISM found 1 hgu95av2PATH2PROBE found 151 hgu95av2PMID2PROBE found 96685 Note that there are zero mappings for hguav2SUMFUNC, hence all should be NA. Best, Jim > > sessionInfo: > > R version 2.2.0, 2005-10-06, i386-pc-mingw32 > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > "datasets" "base" > > other attached packages: > hgu95av2 annotate rat2302 reposTools affy annaffy > KEGG GO Biobase RWinEdt > "1.10.0" "1.8.0" "1.8.5" "1.8.0" "1.8.1" "1.2.0" > "1.8.1" "1.6.5" "1.8.0" "1.7-3" > > Example code used: > > if (require(hgu95av2)) { > data(aafExpr) > probes <- geneNames(aafExpr) > functions <- aafFunction(probes, "hgu95av2") > show(functions[6:10]) > } > > Results: > > An object of class "aafList" > [[1]] > An object of class "aafFunction" > character(0) > > [[2]] > An object of class "aafFunction" > character(0) > > [[3]] > An object of class "aafFunction" > character(0) > > [[4]] > An object of class "aafFunction" > character(0) > > [[5]] > An object of class "aafFunction" > character(0) > > Mark W. Kimpel MD > > > > Official Business Address: > > > > Department of Psychiatry > > Indiana University School of Medicine > > Biotechnology, Research, & Training Center > > 1345 W. 16th Street > > Indianapolis, IN 46202 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623