The CSV files do not seem to follow a standard that R would be able to read
"out of the box"...

They contain records like the following:

"field1","field2","field3a field3b" field3c","field4"

That one quote right after field3b is what messes up with the ability of
properly reading the file... After fixing the file (outside R), I'm able to
properly build the packages (without any change to the pdInfoBuilder
package).

You may want to take into the account the note that came with the files
that states: "Theses files are provided to supply preliminary annotation
information to be used with new gene-level designs until the full NETAFFX
annotations are available"... and hope that once the netaffx annts are
ready, the files will not have such issue....

benilton

On 15 March 2012 15:25, Benilton Carvalho <beniltoncarvalho@gmail.com>wrote:

> 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@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@wur.nl<mailto:Philip.deGroot@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@wur.nl<mailto:Philip.deGroot@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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

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