On Feb 5, 2008, at 8:30 PM, Owen Thomas wrote: > Hi, > > I am trying both the MF and the MR of the version 4 of the yeast > library file. > > I downloaded these from the affymetrix web site: > > http://www.affymetrix.com/support/technical/libraryfilesmain.affx > > I cannot find the version you are using and would be interested to > know how you got it. Ben is using both version 3 and version 4 (as you are), this is evident from his text and the filenames. Kasper > Thanks for your help, > > Regards, > > Owen. > > > On 06/02/2008, at 2:58 PM, Ben Bolstad wrote: > >> At least on my machine the version 3 of this file parses fine: >> >>> library(affyio) >>> bpmap <- .Call ("ReadBPMAPFileIntoRList", "Sc03b_MF_v03.bpmap") >>> sessionInfo() >> R version 2.7.0 Under development (unstable) (2008-02-02 r44303) >> x86_64-unknown-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_U >> S >> .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US >> . >> UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF- >> 8 >> ;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] affyio_1.7.9 >>> names(bpmap) >> [1] "Header" "SequenceDescription" "SeqHead.PosInfo" >>> bpmap$Header >> $magic.number >> [1] "PHT7\r\n\032\n" >> >> $version >> [1] 2 >> >> $n.seq >> [1] 87 >> >>> >> >> >> Digging around for the v4 of this file (again no problem) >> >>> bpmap <- .Call ("ReadBPMAPFileIntoRList", "Sc03b_MF_v04.bpmap") >>> bpmap$Header >> $magic.number >> [1] "PHT7\r\n\032\n?" >> >> $version >> [1] 2 >> >> $n.seq >> [1] 87 >> >> >> >> >> On Tue, 2008-02-05 at 22:50 -0500, Benilton Carvalho wrote: >>> Unless you have other reasons to use R-2.7.0, don't do that... It'll >>> automatically download devel versions of BioConductor packages, and >>> it's hard to guarantee that they will be stable enough.... >>> >>> I'd need to find the BPMAP you're working with, so debugging will >>> simplified... is it at affy's website? where exactly? >>> >>> thanks, >>> >>> b >>> >>> >>> >>> On Feb 5, 2008, at 10:32 PM, Owen Thomas wrote: >>> >>>> I downloaded the affyio 1.7.10 source and installed, but I still >>>> have exactly the same error, which occurs in the >>>> ReadBPMAPFileIntoRList c function: >>>> >>>> bpmap <- .Call ("ReadBPMAPFileIntoRList", "Sc03b_MF_v04.bpmap") >>>> Error: SET_VECTOR_ELT() can only be applied to a 'list', not a >>>> 'NULL' >>>> >>>> It seems that the Mac OS X binary of affyio 1.7.1 is compiled >>>> against a development version of R, would you recommend >>>> upgrading my >>>> version of R? >>>> >>>> Anyway, to confirm the installation my sessionInfo is >>>> >>>>> sessionInfo () >>>> R version 2.6.1 (2007-11-26) >>>> powerpc-apple-darwin8.10.1 >>>> >>>> locale: >>>> C >>>> >>>> attached base packages: >>>> [1] splines tools stats graphics grDevices utils >>>> datasets >>>> [8] methods base >>>> >>>> other attached packages: >>>> [1] makePlatformDesign_1.2.0 oligo_1.2.2 >>>> oligoClasses_1.0.3 >>>> [4] affxparser_1.10.2 AnnotationDbi_1.0.6 >>>> preprocessCore_1.0.0 >>>> [7] RSQLite_0.6-4 DBI_0.2-4 >>>> Biobase_1.16.2 >>>> [10] affyio_1.7.10 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] rcompgen_0.1-17 >>>> >>>> >>>> Regards, >>>> >>>> Owen. >>>> >>>> >>>> On 06/02/2008, at 2:03 PM, Benilton Carvalho wrote: >>>> >>>>> Do you want to try a non-recommended approach? >>>>> >>>>> Install the devel version of affyio, I recall Ben fixing something >>>>> like this not long ago: >>>>> >>>>> http://www.bioconductor.org/packages/2.2/bioc/html/affyio.html >>>>> >>>>> Please let us know how it goes... >>>>> >>>>> b >>>>> >>>>> On Feb 5, 2008, at 9:43 PM, Owen Thomas wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I am running affyio 1.6.1, >>>>>> >>>>>> as confirmed by the sessionInfo: >>>>>> >>>>>>> sessionInfo () >>>>>> R version 2.6.1 (2007-11-26) >>>>>> powerpc-apple-darwin8.10.1 >>>>>> >>>>>> locale: >>>>>> C >>>>>> >>>>>> attached base packages: >>>>>> [1] splines tools stats graphics grDevices utils >>>>>> datasets >>>>>> [8] methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] makePlatformDesign_1.2.0 oligo_1.2.2 >>>>>> oligoClasses_1.0.3 >>>>>> [4] affxparser_1.10.2 AnnotationDbi_1.0.6 >>>>>> preprocessCore_1.0.0 >>>>>> [7] RSQLite_0.6-4 DBI_0.2-4 >>>>>> Biobase_1.16.2 >>>>>> [10] affyio_1.6.1 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] rcompgen_0.1-17 >>>>>> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Owen. >>>>>> >>>>>> On 06/02/2008, at 1:30 PM, Benilton Carvalho wrote: >>>>>> >>>>>>> You didn't provide the results of your sessionInfo() >>>>>>> >>>>>>> But the error is given by affyio, suggesting that you're running >>>>>>> an outdated version (the latest of affyio is 1.6.1). >>>>>>> >>>>>>> Please, ensure you're running this version and let us know what >>>>>>> your sessionInfo() is. >>>>>>> >>>>>>> best, >>>>>>> b >>>>>>> >>>>>>> >>>>>>> On Feb 5, 2008, at 9:11 PM, Owen Thomas wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> I am having trouble using the makePDpackage function, other >>>>>>>> people >>>>>>>> have had the same problem: >>>>>>>> >>>>>>>> https://stat.ethz.ch/pipermail/bioconductor/2008-January/ >>>>>>>> 020922.html >>>>>>>> >>>>>>>> I have found no solution though, if anyone could help me >>>>>>>> understand >>>>>>>> what's going on I would greatly appreciate it. >>>>>>>> >>>>>>>> The concise problem is: >>>>>>>> >>>>>>>> makePDpackage ("Sc03b_MF_v04.bpmap", file1="Sc03b_MF_v04.cif", >>>>>>>> manufacturer="affymetrix", type="tiling") >>>>>>>> affymetrix tiling >>>>>>>> >>>>>>>> The package will be called pd.sc03b.mf.v04 >>>>>>>> >>>>>>>> Error in makeBPMAPenv(designFile, file1, genomebuild = >>>>>>>> genomebuild) : >>>>>>>> SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL' >>>>>>>> >>>>>>>> Thanks, >>>>>>>> >>>>>>>> Owen. >>>>>>>> >>>>>>>> Full R session: >>>>>>>> >>>>>>>> R version 2.6.1 (2007-11-26) >>>>>>>> Copyright (C) 2007 The R Foundation for Statistical Computing >>>>>>>> ISBN 3-900051-07-0 >>>>>>>> >>>>>>>> R is free software and comes with ABSOLUTELY NO WARRANTY. >>>>>>>> You are welcome to redistribute it under certain conditions. >>>>>>>> Type 'license()' or 'licence()' for distribution details. >>>>>>>> >>>>>>>> Natural language support but running in an English locale >>>>>>>> >>>>>>>> R is a collaborative project with many contributors. >>>>>>>> Type 'contributors()' for more information and >>>>>>>> 'citation()' on how to cite R or R packages in publications. >>>>>>>> >>>>>>>> Type 'demo()' for some demos, 'help()' for on-line help, or >>>>>>>> 'help.start()' for an HTML browser interface to help. >>>>>>>> Type 'q()' to quit R. >>>>>>>> >>>>>>>>> library (makePlatformDesign) >>>>>>>> Loading required package: affyio >>>>>>>> Loading required package: oligo >>>>>>>> Loading required package: Biobase >>>>>>>> Loading required package: tools >>>>>>>> >>>>>>>> Welcome to Bioconductor >>>>>>>> >>>>>>>> Vignettes contain introductory material. To view, type >>>>>>>> 'openVignette()'. To cite Bioconductor, see >>>>>>>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>>>>>>> >>>>>>>> Loading required package: splines >>>>>>>> Loading required package: RSQLite >>>>>>>> Loading required package: DBI >>>>>>>> Loading required package: preprocessCore >>>>>>>> Loading required package: AnnotationDbi >>>>>>>> Loading required package: affxparser >>>>>>>> Loading required package: oligoClasses >>>>>>>> This is the oligo package >>>>>>>>> makePDpackage ("Sc03b_MF_v04.bpmap", file1="Sc03b_MF_v04.cif", >>>>>>>> manufacturer="affymetrix", type="tiling") >>>>>>>> affymetrix tiling >>>>>>>> The package will be called pd.sc03b.mf.v04 >>>>>>>> Error in makeBPMAPenv(designFile, file1, genomebuild = >>>>>>>> genomebuild) : >>>>>>>> SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL' >>>>>>>>> traceback () >>>>>>>> 3: .Call("ReadBPMAPFileIntoRList", bpmapFile, PACKAGE = >>>>>>>> "affyio") >>>>>>>> 2: makeBPMAPenv(designFile, file1, genomebuild = genomebuild) >>>>>>>> 1: makePDpackage("Sc03b_MF_v04.bpmap", file1 = >>>>>>>> "Sc03b_MF_v04.cif", >>>>>>>> manufacturer = "affymetrix", type = "tiling") >>>>>>>> >>>>>>>> ____________________________________________________________ >>>>>>>> Receive Notifications of Incoming Messages >>>>>>>> Easily monitor multiple email accounts & access them with a >>>>>>>> click. >>>>>>>> Visit http://www.inbox.com/notifier and check it out! >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>>>>> >>>>>> >>>>> >>>> >>> >> > > _______________________________________________ > 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