Not yet supported, but thinking of a solution.


2013/9/13 He, Yiwen (NIH/CIT) [C] <heyiwen@mail.nih.gov>

> Hi,
>
> I am trying to analyze the affy HTA 2.0 array. I tried to create the
> pd.hta.2.0 package using makePdInfoPackage() in the pdInfoBuilder package,
> and got a message saying data type mismatch. I searched the archive and saw
> people with the same problem, but no solutions. Can someone please help? I
> am using R 3.0.1 and all packages are updated. Thank you!
>
> Yiwen
> NIH/CIT
>
> ---------------------------------------
> library(pdInfoBuilder)
>
> pgf <- "HTA-2_0.r1.pgf"
> clf <- "HTA-2_0.r1.clf"
> probe <- "HTA-2_0.na33.hg19.probeset.csv"
> transcript <- "HTA-2_0.na33.hg19.transcript.csv"
> mps <- "HTA-2_0.r1.Psrs.mps"
>
> seed <- new("AffyGenePDInfoPkgSeed",
>         pgfFile=pgf, clfFile=clf,
>         probeFile=probe,
>         transFile=transcript,
>         coreMps=mps)
>
> makePdInfoPackage(seed, destDir=".", unlink=TRUE)
>
>
> ================================================================================
> Building annotation package for Affymetrix Gene ST Array
> PGF.........: HTA-2_0.r1.pgf
> CLF.........: HTA-2_0.r1.clf
> Probeset....: HTA-2_0.na33.hg19.probeset.csv
> Transcript..: HTA-2_0.na33.hg19.transcript.csv
> Core MPS....: HTA-2_0.r1.Psrs.mps
>
> ================================================================================
> Parsing file: HTA-2_0.r1.pgf... OK
> Parsing file: HTA-2_0.r1.clf... OK
> Creating initial table for probes... OK
> Creating dictionaries... OK
> Parsing file: HTA-2_0.na33.hg19.probeset.csv... OK
> Parsing file: HTA-2_0.r1.Psrs.mps... OK
> Creating package in ./pd.hta.2.0
> Inserting 850 rows into table chrom_dict... OK
> Inserting 5 rows into table level_dict... OK
> Inserting 11 rows into table type_dict... OK
> Inserting 577432 rows into table core_mps... OK
> Inserting 1839617 rows into table featureSet... Error in
> sqliteExecStatement(con, statement, bind.data) :
>   RS-DBI driver: (RS_SQLite_exec: could not execute: datatype mismatch)
>
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