Dear all, i tried to create a PD design for the affy drosphila tiling 1 array but failed due to memory allocation errors (running dual quad mac pro with 18 GB RAM.. wondering). Anyone in here managed to create this package and willing to contribute? thanks in advance! ====================================================================== Dr. Tobias Straub Adolf-Butenandt-Institute, Molecular Biology tel: +49-89-2180 75 439 Schillerstr. 44, 80336 Munich, Germany

Hi Dr. Straub, On Jun 14, 2008, at 7:31 AM, Tobias Straub wrote: > Dear all, > > i tried to create a PD design for the affy drosphila tiling 1 array > but failed due to memory allocation errors (running dual quad mac > pro with 18 GB RAM.. wondering). > > Anyone in here managed to create this package and willing to > contribute? I've previously been able to make PD designs for both the v1 MF and the MR chips. I'm not sure what the secret sauce was, but I built them on our "big iron" servers (64gb ram :-) .. I'd be surprised if the 18gb ram you have wouldn't be sufficient, though. I'm not sure what's going south with your build, but in the meantime you can find the ones that I've built here: http://cbio.mskcc.org/~lianos/files/bioconductor/ They've been built on a 64-bit linux machine. I'm not sure if that's going to affect you or not. HTH, -steve

Hi Benilton, thanks for the tip. unfortunately it did not work due to some unique primary key issue. maybe the bpmap is not compatible with makePdInfoPackage? > bpmapFile <- "Dm35b_MR_v02-3_BDGPv4h.bpmap" > cifFile <- "Dm35b_MR_v02.cif" > obj <- new("AffyTilingPDInfoPkgSeed", + version="0.0.1", + author="TS", email="tobias.straub at lmu.de", + biocViews="AnnotationData", + genomebuild="dmel2", + bpmapFile=bpmapFile, + cifFile=cifFile) > > makePdInfoPackage(obj, destDir=".") Creating package in ./pd.dm35b.mr.v02.3.bdgpv4h Error in sqliteExecStatement(conn, statement, bind.data, ...) : RS-DBI driver: (RS_SQLite_exec: could not execute: PRIMARY KEY must be unique) Timing stopped at: 360.57 63.785 424.923 > traceback() 14: .Call("RS_SQLite_exec", conId, statement, bind.data, PACKAGE = .SQLitePkgName) 13: sqliteExecStatement(conn, statement, bind.data, ...) 12: is(object, Cl) 11: is(object, Cl) 10: .valueClassTest(standardGeneric("dbSendPreparedQuery"), "DBIResult", "dbSendPreparedQuery") 9: dbSendPreparedQuery(db, sql, batchMat[isPm, ]) 8: loadUnits.affyTiling(db, vvunits, nx = nx) 7: loadUnitsByBatch.affyTiling(db, bpmapFile, batch_size = batch_size, nx = nx) 6: eval(expr, envir, enclos) 5: eval(expr, envir = loc.frame) 4: ST(loadUnitsByBatch.affyTiling(db, bpmapFile, batch_size = batch_size, nx = nx)) 3: buildPdInfoDb.affyTiling(object at bpmapFile, object at cifFile, dbFilePath, seqMatFile, batch_size = batch_size, verbose = !quiet) 2: makePdInfoPackage(obj, destDir = ".") 1: makePdInfoPackage(obj, destDir = ".") > sessionInfo() R version 2.7.0 (2008-04-22) i386-apple-darwin8.10.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] pdInfoBuilder_1.4.0 oligo_1.4.0 oligoClasses_1.2.0 [4] AnnotationDbi_1.2.1 preprocessCore_1.2.0 affxparser_1.12.2 [7] RSQLite_0.6-8 DBI_0.2-4 Biobase_2.0.1 On Jun 14, 2008, at 9:47 PM, Benilton Carvalho wrote: > Hi Tobias, > > you should try using the pdInfoBuilder package instead. > > The following code works fine for me (for a promoter array) and i > don't foresee any reason for it not work with the drosophila array > (with the appropriate changes). > > ### > library(pdInfoBuilder) > bpmapFile <- "Hs_PromPR_v02-3_NCBIv36.bpmap" > cifFile <- "Hs_PromPR_v02.cif" > > obj <- new("AffyTilingPDInfoPkgSeed", > version="0.0.1", > author="Benilton Carvalho", email="bcarvalh at jhsph.edu", > biocViews="AnnotationData", > genomebuild="NCBI Build 36", > bpmapFile=bpmapFile, > cifFile=cifFile) > makePdInfoPackage(obj, destDir=".") > ### > > please, let me know how it goes, > > best, > b > > > On Jun 14, 2008, at 7:31 AM, Tobias Straub wrote: > >> Dear all, >> >> i tried to create a PD design for the affy drosphila tiling 1 array >> but failed due to memory allocation errors (running dual quad mac >> pro with 18 GB RAM.. wondering). >> >> Anyone in here managed to create this package and willing to >> contribute? >> >> thanks in advance! >> >> = >> ===================================================================== >> Dr. Tobias Straub Adolf-Butenandt-Institute, Molecular >> Biology >> tel: +49-89-2180 75 439 Schillerstr. 44, 80336 Munich, >> Germany >> >> _______________________________________________ >> 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 > ====================================================================== Dr. Tobias Straub Adolf-Butenandt-Institute, Molecular Biology tel: +49-89-2180 75 439 Schillerstr. 44, 80336 Munich, Germany