Question: problem with pdInfoBuilder
0
gravatar for Elsa Aguera
10.4 years ago by
Elsa Aguera10
Elsa Aguera10 wrote:
Hi everybody ! I try to build a package to use oligo. so for that I use pdInfoBuilder and a bpmap file. I work on a tiling array from affymetrix. here is my sessionInfo() : > sessionInfo() R version 2.9.0 (2009-04-17) i486-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pdInfoBuilder_1.8.1 preprocessCore_1.6.0 oligoClasses_1.5.23 [4] RSQLite_0.7-1 DBI_0.2-4 AffyTiling_1.2.0 [7] Biobase_2.4.1 aroma.affymetrix_1.0.0 aroma.apd_0.1.3 [10] R.huge_0.1.7 affxparser_1.16.0 aroma.core_1.0.4 [13] aroma.light_1.13.1 oligo_1.8.1 affy_1.22.0 [16] digest_0.3.1 matrixStats_0.1.4 R.rsp_0.3.4 [19] R.cache_0.1.7 R.utils_1.1.5 R.oo_1.4.6 [22] R.methodsS3_1.0.3 loaded via a namespace (and not attached): [1] affyio_1.8.1 Biostrings_2.12.3 IRanges_1.1.68 splines_2.9.0 [5] tcltk_2.9.0 tools_2.9.0 here is my code : > makePdInfoPackage(seed, destDir=".") ====================================================================== ========== Building annotation package for Affymetrix Tiling array BPMAP: Dm_tiling2_MR_v01.bpmap CEL..: gfpa4.CEL ====================================================================== ========== Parsing file: Dm_tiling2_MR_v01.bpmap ... OK Getting geometry from CEL file... OK Getting PMs...OK Getting MMs...OK Getting background probes...OK Getting sequences...OK Creating package in ./pd.dm.tiling2.mr.v01 Inserting 18 rows into table "chrom_dict"... OK Inserting 2870706 rows into table "pmfeature"... Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (RS_SQLite_exec: could not execute: PRIMARY KEY must be unique) I don't know why I have this error does anybody help ? thanks elsa _________________________________________________________________ ? Lancez-vous ! [[alternative HTML version deleted]]
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