 Dear all,

I am trying to create the pfInfoBuilder packages for Affy's GeneChip Human
Transcriptome Array 2.0.

I am using the "original" pgf, clf, mps, and probeset.csv files from the
library files from Affy's website (
http://www.affymetrix.com/Auth/analysis/downloads/lf/hta/HTA-2_0/AGCC_library_installer_HTA-2_0.zip
).

I was able to read the probeset.csv file using plain vanilla read.csv.
        Thus, it is likely the solution given to a similar problem with
Arabidopsis chips does not apply ("pdInfoBuilder fails on the new
Arabidopsis Gene ST 1.0 & 1.1 arrays",
https://stat.ethz.ch/pipermail/bioconductor/2012-March/044231.html)

Details are shown below.

        Any help greatly appreciated.

Regards,

Guilherme Rocha


------------------------------------------------------------------------------------------------------------
R Code and output:

> library(pdInfoBuilder)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

    xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq,
    get, intersect, is.unsorted, lapply, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rep.int,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unlist

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RSQLite
Loading required package: DBI
Loading required package: affxparser
Loading required package: oligo
Loading required package: oligoClasses
Welcome to oligoClasses version 1.24.0
================================================================================
Welcome to oligo version 1.26.0
================================================================================

Attaching package: 'oligo'

The following object is masked from 'package:BiocGenerics':

    normalize

>
> base_dir = "./"
>
> pgf          = paste(base_dir, "/HTA-2_0.r1.pgf", sep="")
> clf          = paste(base_dir, "/HTA-2_0.r1.clf", sep="")
> prob         = paste(base_dir, "/HTA-2_0.na33.hg19.probeset.csv", sep="")
> core_mps     = paste(base_dir, "/HTA-2_0.r1.Psrs.mps", sep="")
> extended_mps = paste(base_dir, "/HTA-2_0.r1.Psrs.mps", sep="")
> full_mps     = paste(base_dir, "/HTA-2_0.r1.Psrs.mps", sep="")
>
> test_csv     = read.csv(paste(base_dir,
"/HTA-2_0.na33.hg19.probeset.csv", sep=""), skip=14, header=T)
>
> seed = new("AffyExonPDInfoPkgSeed",
+            pgfFile     = pgf,
+            clfFile     = clf,
+            probeFile   = prob,
+            coreMps     = core_mps,
+            extendedMps = extended_mps,
+            fullMps     = full_mps,
+            author      = "GR",
+            email       = "anemailadress@gmail.com",
+            biocViews   = "AnnotationData",
+            genomebuild = "GRCh37",
+            organism    = "Human",
+            species     = "Homo sapiens",
+            url         = "")
>
> makePdInfoPackage(seed, destDir=base_dir);
================================================================================
Building annotation package for Affymetrix Exon ST Array
PGF.........: HTA-2_0.r1.pgf
CLF.........: HTA-2_0.r1.clf
Probeset....: HTA-2_0.na33.hg19.probeset.csv
Transcript..: TheTranscriptFile
Core MPS....: HTA-2_0.r1.Psrs.mps
Full MPS....: HTA-2_0.r1.Psrs.mps
Extended 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
Parsing file: HTA-2_0.r1.Psrs.mps... 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 577432 rows into table full_mps... OK
Inserting 577432 rows into table extended_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)
>
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] pdInfoBuilder_1.26.0 oligo_1.26.0         oligoClasses_1.24.0
[4] affxparser_1.34.0    RSQLite_0.11.4       DBI_0.2-7
[7] Biobase_2.22.0       BiocGenerics_0.8.0

loaded via a namespace (and not attached):
 [1] BiocInstaller_1.12.0  Biostrings_2.30.0     GenomicRanges_1.14.1
 [4] IRanges_1.20.0        XVector_0.2.0         affyio_1.30.0
 [7] bit_1.1-10            codetools_0.2-8       ff_2.2-12
[10] foreach_1.4.1         iterators_1.0.6       preprocessCore_1.24.0
[13] splines_3.0.2         stats4_3.0.2          zlibbioc_1.8.0

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