[BioC] Affy HTA 2.0 array analysis

[He, Yiwen (NIH/CIT) [C]]

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)