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

Thu Mar 15 16:25:39 CET 2012

I'll get back to the list once I've addressed the problem. benilton

On 14 March 2012 11:11, Groot, Philip de <philip.degroot at wur.nl> wrote:
> 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.
>
>
>
> Regards,
>
>
>
> 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/>
> http://humannutrition.wur.nl/
> https://madmax.bioinformatics.nl/
>
>
>
>
>
> Information regarding the chip on the Affymetrix website:
> Design time annotation file:
> http://www.affymetrix.com/Auth/analysis/downloads/na32/wtgene/AraGene-1_0-st-v1.annotations.design-time.20111019.zip
>
> Library files:
> http://www.affymetrix.com/Auth/analysis/downloads/lf/wt/AraGene-1_0-st-v1/AraGene-1_0-st_rev01.zip
>
>
>
> 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)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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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