Hi Yu-An, I still cannot reproduce the same error even I switch to an i686-pc-linux-gnu machine. Here are some suggestions: (1) re-install GO package (2) not using the natural language support. Use English for your R and try again. HTH, Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA ______________________________________ On Sat, 28 Jan 2006, Yu-An Dong wrote: > Hi Ting-Yuan, > > I still get the same problem, e.g. > > > GOLOCUSID2GO[["4121"]] > Fehler: rekursive Standardargument Referenz > > The error message says: "Error: recursive standard argument reference". Here's > my > session info: > > > sessionInfo() > R version 2.2.0, 2005-10-06, i686-pc-linux-gnu > > attached base packages: > [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" > [7] "utils" "datasets" "base" > > other attached packages: > hgu95av2 GOstats multtest genefilter survival xtable RBGL > "1.10.0" "1.4.0" "1.8.0" "1.8.0" "2.20" "1.3-0" "1.6.0" > annotate Biobase GO graph Ruuid cluster > "1.8.0" "1.8.0" "1.10.0" "1.8.0" "1.8.0" "1.10.2" > > Any suggestions? Thanks! > > Yu-An > > > > Ting-Yuan Liu wrote: > > Hi Yu-An, > > > > I think the error message is not written in English, right? Could you > > translate it to English so that it will be more helpful. > > > > I cannot reproduce the same error in my machine, and here is the result: > > > > > GOLOCUSID2GO[["4121"]] > > > > > $"GO:0005975" > > $"GO:0005975"$GOID > > IEA > > "GO:0005975" > > > > $"GO:0005975"$Evidence > > [1] "IEA" > > > > $"GO:0005975"$Ontology > > [1] "BP" > > > > > > $"GO:0006487" > > $"GO:0006487"$GOID > > IEA > > "GO:0006487" > > > > $"GO:0006487"$Evidence > > [1] "IEA" > > > > $"GO:0006487"$Ontology > > [1] "BP" > > > > .... skip ... > > > > Here is the result of my sessionInfo(): > > > > > sessionInfo() > > > > > R version 2.2.1, 2006-01-04, x86_64-unknown-linux-gnu > > > > attached base packages: > > [1] "methods" "stats" "graphics" "grDevices" "utils" > > "datasets" > > [7] "base" > > > > other attached packages: > > GO > > "1.10.0" > > > > > > Could you also provide the sessionInfo() output for more information > > please? Thanks. > > > > Ting-Yuan > > ______________________________________ > > Ting-Yuan Liu > > Program in Computational Biology > > Division of Public Health Sciences > > Fred Hutchinson Cancer Research Center > > Seattle, WA, USA > > ______________________________________ > > > > On Wed, 25 Jan 2006, Yu-An Dong wrote: > > > > > > > Hello, I've installed BioC 1.7 (with R 2.2.0) without problem. The GO > > > package was installed but I can't > > > access the data: > > > > > > > GOLOCUSID2GO[["4121"]] > > > Fehler: rekursive Standardargument Referenz > > > > > > And I get similar error messages with the other functions in the GO > > > package. Any suggestions? Thanks! > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > >

Hi, start a clean R and make sure it does not load any save workspaces. [If you see this message: [Previously saved workspace restored] then you need to move to a different directory to start or move the saved workspace so it is not automatically loaded] then go library(GO) GOLOCUSID2GO[["4121"]] if you get an error report it and the output of traceback(). And if not, then it is not GO, it is something else, probably a variable you have created (or that someone else has) that is interfering with dispatch in some odd way. To find out who/what, start adding the libraries you have listed, one at a time until the culprit is found. best wishes Robert Yu-An Dong wrote: > Hi Ting-Yuan, > > I still get the same problem, e.g. > > > GOLOCUSID2GO[["4121"]] > Fehler: rekursive Standardargument Referenz > > The error message says: "Error: recursive standard argument reference". > Here's my > session info: > > > sessionInfo() > R version 2.2.0, 2005-10-06, i686-pc-linux-gnu > > attached base packages: > [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" > [7] "utils" "datasets" "base" > > other attached packages: > hgu95av2 GOstats multtest genefilter survival xtable RBGL > "1.10.0" "1.4.0" "1.8.0" "1.8.0" "2.20" "1.3-0" "1.6.0" > annotate Biobase GO graph Ruuid cluster > "1.8.0" "1.8.0" "1.10.0" "1.8.0" "1.8.0" "1.10.2" > > Any suggestions? Thanks! > > Yu-An > > > > Ting-Yuan Liu wrote: > >>Hi Yu-An, >> >>I think the error message is not written in English, right? Could you >>translate it to English so that it will be more helpful. >> >>I cannot reproduce the same error in my machine, and here is the result: >> >> >>>GOLOCUSID2GO[["4121"]] >>> >> >>$"GO:0005975" >>$"GO:0005975"$GOID >> IEA >>"GO:0005975" >> >>$"GO:0005975"$Evidence >>[1] "IEA" >> >>$"GO:0005975"$Ontology >>[1] "BP" >> >> >>$"GO:0006487" >>$"GO:0006487"$GOID >> IEA >>"GO:0006487" >> >>$"GO:0006487"$Evidence >>[1] "IEA" >> >>$"GO:0006487"$Ontology >>[1] "BP" >> >>.... skip ... >> >>Here is the result of my sessionInfo(): >> >> >>>sessionInfo() >>> >> >>R version 2.2.1, 2006-01-04, x86_64-unknown-linux-gnu >> >>attached base packages: >>[1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" >>[7] "base" >> >>other attached packages: >> GO >>"1.10.0" >> >> >>Could you also provide the sessionInfo() output for more information >>please? Thanks. >> >>Ting-Yuan >>______________________________________ >>Ting-Yuan Liu >>Program in Computational Biology >>Division of Public Health Sciences >>Fred Hutchinson Cancer Research Center >>Seattle, WA, USA >>______________________________________ >> >>On Wed, 25 Jan 2006, Yu-An Dong wrote: >> >> >> >>>Hello, I've installed BioC 1.7 (with R 2.2.0) without problem. The GO >>>package was installed but I can't >>>access the data: >>> >>> > GOLOCUSID2GO[["4121"]] >>>Fehler: rekursive Standardargument Referenz >>> >>>And I get similar error messages with the other functions in the GO >>>package. Any suggestions? Thanks! >>> >>>_______________________________________________ >>>Bioconductor mailing list >>>Bioconductor at stat.math.ethz.ch >>>https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >>> > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

You are confusing an annotation package with a cdf package. The annotation package contains all the symbols, where the cdf package contains information about which probes are PM/MM and how they are bundled together in probesets (probing genes). Use hgu133plus2 instead, and just for the sake of it, compare hgu133plus with hgu95av2 and hgu133plus2cdf with hgu95av2cdf There is a third kind of package, the probe package (hgu133plus2probe) containing information on the actual sequences synthezised on the array. /Kasper On Jan 30, 2006, at 8:18 PM, jsv at stat.ohio-state.edu wrote: > I'm having trouble getting symbols for this chip. I've loaded the > hgu133plus2cdf package: > >> sessionInfo() > R version 2.2.0, 2005-10-06, i386-pc-mingw32 > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" > "utils" > "datasets" > [8] "base" > > other attached packages: > hgu95av2 annaffy KEGG GO > hgu133plus2cdf > affy > "1.10.0" "1.2.0" "1.10.0" "1.10.0" > "1.10.0" > "1.8.1" > Biobase > "1.8.0" > > The problem comes when I try > >> g.symbols <- aafSymbol(gn,"hgu133plus2cdf") > Error in mget(c("1007_s_at", "1053_at", "117_at", "121_at", > "1255_g_at", : > object "hgu133plus2cdfSYMBOL" not found > > > The package has the following objects: > >> objects("package:hgu133plus2cdf") > [1] "hgu133plus2cdf" "i2xy" "xy2i" > > This seems particularly sparse, compared to, say, > > objects("package:hgu95av2") > [1] "hgu95av2" "hgu95av2ACCNUM" "hgu95av2CHR" > "hgu95av2CHRLENGTHS" > [5] "hgu95av2CHRLOC" "hgu95av2ENZYME" > "hgu95av2ENZYME2PROBE" > "hgu95av2GENENAME" > [9] "hgu95av2GO" "hgu95av2GO2ALLPROBES" "hgu95av2GO2PROBE" > "hgu95av2LOCUSID" > [13] "hgu95av2MAP" "hgu95av2MAPCOUNTS" "hgu95av2OMIM" > "hgu95av2ORGANISM" > [17] "hgu95av2PATH" "hgu95av2PATH2PROBE" "hgu95av2PFAM" > "hgu95av2PMID" > [21] "hgu95av2PMID2PROBE" "hgu95av2PROSITE" "hgu95av2QC" > "hgu95av2QCDATA" > [25] "hgu95av2REFSEQ" "hgu95av2SUMFUNC" "hgu95av2SYMBOL" > "hgu95av2UNIGENE" > > > Interestingly, > > g.symbols <- aafSymbol(gn,"hgu95av2") > > finds about 300 gene symbols using the older probe identifiers. > > Any help on finding and loading the latest version of > hgu133plus2cdf onto > a Windows XP system, or finding some other way to get the symbols > would be > much appreciated. > > Joe Verducci > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor

jsv at stat.ohio-state.edu wrote: > I'm having trouble getting symbols for this chip. I've loaded the > hgu133plus2cdf package: The problem arises from the fact that you are loading and using the hgu133plus2cdf package rather than the hgu133plus2 package, which is what you want. 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" > [8] "base" > > other attached packages: > hgu95av2 annaffy KEGG GO hgu133plus2cdf > affy > "1.10.0" "1.2.0" "1.10.0" "1.10.0" "1.10.0" > "1.8.1" > Biobase > "1.8.0" > > The problem comes when I try > > >>g.symbols <- aafSymbol(gn,"hgu133plus2cdf") > > Error in mget(c("1007_s_at", "1053_at", "117_at", "121_at", "1255_g_at", : > object "hgu133plus2cdfSYMBOL" not found > > > The package has the following objects: > > >>objects("package:hgu133plus2cdf") > > [1] "hgu133plus2cdf" "i2xy" "xy2i" > > This seems particularly sparse, compared to, say, > > objects("package:hgu95av2") > [1] "hgu95av2" "hgu95av2ACCNUM" "hgu95av2CHR" > "hgu95av2CHRLENGTHS" > [5] "hgu95av2CHRLOC" "hgu95av2ENZYME" "hgu95av2ENZYME2PROBE" > "hgu95av2GENENAME" > [9] "hgu95av2GO" "hgu95av2GO2ALLPROBES" "hgu95av2GO2PROBE" > "hgu95av2LOCUSID" > [13] "hgu95av2MAP" "hgu95av2MAPCOUNTS" "hgu95av2OMIM" > "hgu95av2ORGANISM" > [17] "hgu95av2PATH" "hgu95av2PATH2PROBE" "hgu95av2PFAM" > "hgu95av2PMID" > [21] "hgu95av2PMID2PROBE" "hgu95av2PROSITE" "hgu95av2QC" > "hgu95av2QCDATA" > [25] "hgu95av2REFSEQ" "hgu95av2SUMFUNC" "hgu95av2SYMBOL" > "hgu95av2UNIGENE" > > > Interestingly, > > g.symbols <- aafSymbol(gn,"hgu95av2") > > finds about 300 gene symbols using the older probe identifiers. > > Any help on finding and loading the latest version of hgu133plus2cdf onto > a Windows XP system, or finding some other way to get the symbols would be > much appreciated. > > Joe Verducci > > _______________________________________________ > 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

Jim makes a good point here. With the system we are currently using, all of the data are stored in files and loaded on demand. That means that the first query is always going to be slow (and possibly really slow on some systems with limited RAM), subsequent queries will be fast. We are working on a new system that will speed things up substantially. Hitting control-C could certainly do odd things (but I would have expected general odd things), like no calls to [[ to work, not just this particular one - now maybe that is the case (and if so, could you let us know Yu-An?) best wishes Robert James W. MacDonald wrote: > Yu-An, > > Could the problem be impatience on your part? On both WinXP and Linux > this takes a bit of time for me (using either R-2.2.0 or R-2.3.0): > > > library(GO) > > system.time(GOLOCUSID2GO[["4121"]]) > [1] 30.94 0.57 31.53 NA NA > > Note that any further queries of this sort take no time at all: > > > system.time(GOLOCUSID2GO[["4121"]]) > [1] 0 0 0 NA NA > > system.time(GOLOCUSID2GO[["4122"]]) > [1] 0 0 0 NA NA > > > Best, > > Jim > > Robert Gentleman wrote: > >> OK, well the next option is to move to the current version of R >> (which is not 2.2.0) and see if your problems persist. I cannot >> replicate the bug on any system I have access to. And since [[ takes >> one argument, it is hard to see how it has a recursive standard >> argument...someone is confused (maybe overoptimized compiling, but >> even that is very rare these days). >> >> Or you to get more serious about debugging. Which will most likely >> involve getting gdb or some similar interface to it working so you can >> probe the internals. >> >> sorry >> Robert >> >> Yu-An Dong wrote: >> >>> Hi Robert, >>> I started R in a clean directory and loaded GO: >>> >>> > library(GO) >>> > GOLOCUSID2GO[["4121"]] >>> >>> However, R simply hanged there and I had to use ^-C to interrupt. But >>> when I issued the command >>> a second time, I immediately got the same error as before: >>> >>> > GOLOCUSID2GO[["4121"]] >>> Fehler: rekursive Standardargument Referenz ("Error: recursive >>> standard argument reference") >>> > traceback() >>> Kein traceback vef?gbar ("No traceback available") >>> >>> > sessionInfo() >>> R version 2.2.0, 2005-10-06, i686-pc-linux-gnu >>> >>> attached base packages: >>> [1] "methods" "stats" "graphics" "grDevices" "utils" >>> "datasets" >>> [7] "base" >>> >>> other attached packages: >>> GO >>> "1.10.0" >>> >>> Mm, strange... Again, I appreciate your help! >>> Best wishes, >>> Yu-An >>> >>> >>> >>> >>> >>> >>> >>> Robert Gentleman wrote: >>> >>> >>>> Hi, >>>> start a clean R and make sure it does not load any save workspaces. >>>> [If you see this message: [Previously saved workspace restored] >>>> then you need to move to a different directory to start or move the >>>> saved workspace so it is not automatically loaded] >>>> >>>> then go >>>> >>>> library(GO) >>>> GOLOCUSID2GO[["4121"]] >>>> >>>> if you get an error report it and the output of traceback(). And if >>>> not, then it is not GO, it is something else, probably a variable >>>> you have created (or that someone else has) that is interfering with >>>> dispatch in some odd way. To find out who/what, start adding the >>>> libraries you have listed, one at a time until the culprit is found. >>>> >>>> >>>> best wishes >>>> Robert >>>> >>>> >>>> Yu-An Dong wrote: >>>> >>>> >>>>> Hi Ting-Yuan, >>>>> >>>>> I still get the same problem, e.g. >>>>> >>>>> > GOLOCUSID2GO[["4121"]] >>>>> Fehler: rekursive Standardargument Referenz >>>>> >>>>> The error message says: "Error: recursive standard argument >>>>> reference". Here's my >>>>> session info: >>>>> >>>>> > sessionInfo() >>>>> R version 2.2.0, 2005-10-06, i686-pc-linux-gnu >>>>> >>>>> attached base packages: >>>>> [1] "splines" "tools" "methods" "stats" "graphics" >>>>> "grDevices" >>>>> [7] "utils" "datasets" "base" >>>>> >>>>> other attached packages: >>>>> hgu95av2 GOstats multtest genefilter survival >>>>> xtable RBGL >>>>> "1.10.0" "1.4.0" "1.8.0" "1.8.0" "2.20" "1.3-0" >>>>> "1.6.0" >>>>> annotate Biobase GO graph Ruuid cluster >>>>> "1.8.0" "1.8.0" "1.10.0" "1.8.0" "1.8.0" "1.10.2" >>>>> >>>>> Any suggestions? Thanks! >>>>> >>>>> Yu-An >>>>> >>>>> >>>>> >>>>> Ting-Yuan Liu wrote: >>>>> >>>>> >>>>>> Hi Yu-An, >>>>>> >>>>>> I think the error message is not written in English, right? Could >>>>>> you translate it to English so that it will be more helpful. >>>>>> >>>>>> I cannot reproduce the same error in my machine, and here is the >>>>>> result: >>>>>> >>>>>> >>>>>> >>>>>>> GOLOCUSID2GO[["4121"]] >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> $"GO:0005975" >>>>>> $"GO:0005975"$GOID >>>>>> IEA >>>>>> "GO:0005975" >>>>>> >>>>>> $"GO:0005975"$Evidence >>>>>> [1] "IEA" >>>>>> >>>>>> $"GO:0005975"$Ontology >>>>>> [1] "BP" >>>>>> >>>>>> >>>>>> $"GO:0006487" >>>>>> $"GO:0006487"$GOID >>>>>> IEA >>>>>> "GO:0006487" >>>>>> >>>>>> $"GO:0006487"$Evidence >>>>>> [1] "IEA" >>>>>> >>>>>> $"GO:0006487"$Ontology >>>>>> [1] "BP" >>>>>> >>>>>> .... skip ... >>>>>> >>>>>> Here is the result of my sessionInfo(): >>>>>> >>>>>> >>>>>> >>>>>>> sessionInfo() >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> R version 2.2.1, 2006-01-04, x86_64-unknown-linux-gnu >>>>>> >>>>>> attached base packages: >>>>>> [1] "methods" "stats" "graphics" "grDevices" "utils" >>>>>> "datasets" >>>>>> [7] "base" >>>>>> >>>>>> other attached packages: >>>>>> GO >>>>>> "1.10.0" >>>>>> >>>>>> >>>>>> Could you also provide the sessionInfo() output for more >>>>>> information please? Thanks. >>>>>> >>>>>> Ting-Yuan >>>>>> ______________________________________ >>>>>> Ting-Yuan Liu >>>>>> Program in Computational Biology >>>>>> Division of Public Health Sciences >>>>>> Fred Hutchinson Cancer Research Center >>>>>> Seattle, WA, USA >>>>>> ______________________________________ >>>>>> >>>>>> On Wed, 25 Jan 2006, Yu-An Dong wrote: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> Hello, I've installed BioC 1.7 (with R 2.2.0) without problem. >>>>>>> The GO package was installed but I can't >>>>>>> access the data: >>>>>>> >>>>>>> >>>>>>>> GOLOCUSID2GO[["4121"]] >>>>>>> >>>>>>> >>>>>>> Fehler: rekursive Standardargument Referenz >>>>>>> >>>>>>> And I get similar error messages with the other functions in the >>>>>>> GO package. Any suggestions? Thanks! >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at stat.math.ethz.ch >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> >>>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> >>>> >>> >> > > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org