Hi Benilton, sorry for my late reply. So I tried it with R 2.12 and 2.10.x and it is always the same problem. If I run R 2.12 and try to create the package using > makePdInfoPackage(pkg, destDir = wd) I get Creating package in /media/0C025E96391493AF/data/FSP_Klein_Pospisil/pd.mousedivm520650 Error in is(object, Cl) : error in evaluating the argument 'bind.data' in selecting a method for function 'dbSendPreparedQuery' Timing stopped at: 22.797 6.852 30.105 And traceback() gives this result: > traceback() 9: is(object, Cl) 8: .valueClassTest(standardGeneric("dbSendPreparedQuery"), "DBIResult", "dbSendPreparedQuery") 7: dbSendPreparedQuery(db, sql, data.frame(pmi = batchMat[isPm, "indices"], mmi = batchMat[!isPm, "indices"])) 6: loadUnits(db, qcunits, isQc = TRUE) 5: loadUnitsByBatch(db, cdfFile, batch_size = batch_size) 4: ST(loadUnitsByBatch(db, cdfFile, batch_size = batch_size)) 3: buildPdInfoDb(object at cdfFile, object at csvAnnoFile, object at csvSeqFile, dbFilePath, seqMatFile, batch_size = batch_size, verbose = !quiet) 2: makePdInfoPackage(pkg, destDir = wd) 1: makePdInfoPackage(pkg, destDir = wd) My SessionInfo is: > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pdInfoBuilder_1.14.1 oligo_1.14.0 oligoClasses_1.12.1 [4] affxparser_1.22.0 RSQLite_0.9-4 DBI_0.2-5 [7] Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 Biostrings_2.18.2 IRanges_1.8.5 [4] preprocessCore_1.12.0 splines_2.12.0 Thanks, Christoph On 12/16/2010 02:18 PM, Benilton Carvalho wrote: > Or, given that you tried with R 2.12, can you please give me the exact > sessionInfo() for that? > > On 16 December 2010 13:17, Benilton Carvalho<beniltoncarvalho at="" gmail.com=""> wrote: > >> Can you please update to the latest R and pdInfoBuilder and let us >> know if the error persists? >> >> Also, note that, although you'll have the annotation package, you >> won't be able to get genotype calls through oligo/crlmm (currently, we >> need training data to train the algorithm). >> >> b >> >> On 16 December 2010 12:44, Christoph Standfu? >> <christoph.standfuss at="" inf.fu-berlin.de=""> wrote: >> >>> Hello, everyone >>> >>> I am currently analysing a couple of Affymetrix Mouse Diversity Genotyping >>> Arrays. Unfortunately there is no annotation package available yet. So I >>> tried to create an own annotation package using pdInfoBuilder, the CDF and >>> annotation files provided by Affymetrix library files. >>> >>> I followed the instructions, given in the manual. Whenever I select >>> "AffySNPPDInfoPkgSeed" as package class, I get the error: >>> >>> >>>> makePdInfoPackage(pkg, destDir = wd) >>>> >>> Creating package in /media/0C025E96391493AF/data/FSP/pd.mousedivm520650 >>> Error in data.frame(pmi = batchMat[isPm, "indices"], mmi = batchMat[!isPm, >>> : >>> arguments imply differing number of rows: 28132, 19132 >>> Error in is(object, Cl) : >>> error in evaluating the argument 'bind.data' in selecting a method for >>> function 'dbSendPreparedQuery' >>> Timing stopped at: 22.109 7.016 29.95" >>> >>> >>> >>> I guess the problem might be that Bioconductor is not able to handle the CDF >>> file correctly? I tried R 2.10.* (bioconductor 2.5) and R 2.12 (bioconductor >>> 2.7), but I had always the same problems. >>> >>> My sessionInfo() is >>> >>> R version 2.10.1 (2009-12-14) >>> i686-pc-linux-gnu >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> Thanks a lot for your help, and best regards, >>> >>> Christoph >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>