[BioC] pdInfoBuilder fails on the new Arabidopsis Gene ST 1.0 & 1.1 arrays

Groot, Philip de philip.degroot at wur.nl
Wed Mar 14 12:11:53 CET 2012

Dear Benilton,

I tried to create the pdInfoBuilder packages for the Affymetrix  Arabidopsis ST 1.0 arrays and did run into a problem that I cannot solve myself. I guess that it also affects the Arabidopsis ST 1.1 cartridges, so you might want to take a look. I pasted the appropriate information below.


Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: Erfelijkheidsleer: De Valk, Building 304
Dreijenweg 2, 6703 HA Wageningen
Room: 0052a
T: +31-317-485786
F: +31-317-483342
E-mail: Philip.deGroot at wur.nl<mailto:Philip.deGroot at wur.nl>
Internet: http://www.nutrigenomicsconsortium.nl<http://www.nutrigenomicsconsortium.nl/>

Information regarding the chip on the Affymetrix website:
Design time annotation file:

Library files:

The code that I utilized in R:

> library("pdInfoBuilder")
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  '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 1.16.0
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
Loading package bit 1.1-8
package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit
Loading package ff2.2-5
- getOption("fftempdir")=="/tmp/RtmpBnumMg"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system

Welcome to oligo version 1.18.1
> pgfFile<-"./AraGene-1_0-st.pgf"
> clfFile<-"./AraGene-1_0-st.clf"
> probeFile<-"./AraGene-1_0-st-v1.design-time.20111019.probeset.csv"
> transFile<-"./AraGene-1_0-st-v1.design-time.20111019.transcript.csv"
> mpsFile <- "./AraGene-1_0-st.mps"
> pkg<-new("AffyGenePDInfoPkgSeed", version="1.0.0", author="Philip de Groot", email="Philip.deGroot at wur.nl<mailto:Philip.deGroot at wur.nl>", chipName="aragene", genomebuild="Tair10", species="Arabidopsis thaliana" , clfFile=clfFile, pgfFile=pgfFile, coreMps=mpsFile, probeFile=probeFile, transFile=transFile)
> makePdInfoPackage(pkg, destDir=".")
Building annotation package for Affymetrix Gene ST Array
PGF.........: AraGene-1_0-st.pgf
CLF.........: AraGene-1_0-st.clf
Probeset....: AraGene-1_0-st-v1.design-time.20111019.probeset.csv
Transcript..: AraGene-1_0-st-v1.design-time.20111019.transcript.csv
Core MPS....: AraGene-1_0-st.mps
Parsing file: AraGene-1_0-st.pgf... OK
Parsing file: AraGene-1_0-st.clf... OK
Creating initial table for probes... OK
Creating dictionaries... OK
Parsing file: AraGene-1_0-st-v1.design-time.20111019.probeset.csv... OK
Parsing file: AraGene-1_0-st.mps... OK
Creating package in ./pd.aragene.1.0.st
Inserting 1200 rows into table chrom_dict... OK
Inserting 5 rows into table level_dict... OK
Inserting 8 rows into table type_dict... OK
Inserting 181946 rows into table core_mps... OK
Inserting 179330 rows into table featureSet... Error in sqliteExecStatement(con, statement, bind.data) :
  RS-DBI driver: (RS_SQLite_exec: could not execute: datatype mismatch)
In addition: Warning messages:
1: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
2: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'

> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

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

other attached packages:
[1] pdInfoBuilder_1.18.0 oligo_1.18.1         oligoClasses_1.16.0
[4] affxparser_1.26.4    RSQLite_0.11.1       DBI_0.2-5
[7] Biobase_2.14.0

loaded via a namespace (and not attached):
[1] affyio_1.22.0         Biostrings_2.22.0     bit_1.1-8
[4] ff_2.2-5              IRanges_1.12.6        preprocessCore_1.16.0
[7] splines_2.14.0        zlibbioc_1.0.1

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