[BioC] makePDpackage affy drosophila tiling 1 array

[Tobias Straub]

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
>>
>> _______________________________________________
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>

======================================================================
Dr. Tobias Straub         Adolf-Butenandt-Institute, Molecular Biology
tel: +49-89-2180 75 439         Schillerstr. 44, 80336 Munich, Germany