[BioC] error using pdInfoBuilder on Affymetrix snp 5.0 array

[Henrik Bengtsson]

On Dec 13, 2007 7:28 AM, James W. MacDonald <jmacdon at med.umich.edu> wrote:
> Hi Sergii,
>
> Sergii Ivakhno wrote:
> > Hello All,
> > I experience a problen when trying to build PDInfo Package for an
> > Affymetrix snp 5.0  array using pdInfoBuilder.
> > Below are my commands, thanks a lot for your assistance in advance!
> > Best Wishes,
> > Sergii
> >
> > library("pdInfoBuilder")
> > cdfFile <- "GenomeWideSNP_5.r2.cdf"
> > csvAnno <- "GenomeWideSNP_5.na24.annot.csv"
> > csvSeq <- "GenomeWideSNP_5.probe_tab"
> > pkg <- new("AffySNPPDInfoPkgSeed", version = "0.1.5",author = "Seth
> > Falcon", email = "sergii.ivakhno at cancer.org.uk",+
> > biocViews = "AnnotationData", genomebuild = "NCBI Build 35, May
> > 2004",cdfFile = cdfFile, csvAnnoFile = csvAnno,csvSeqFile = csvSeq)
> >
> >> makePdInfoPackage(pkg, destDir = ".")
> > Creating package in ./pd.genomewidesnp.5
> > Error in sqliteExecStatement(conn, statement, bind.data, ...) :
> >         RS-DBI driver: (incomplete data binding: expected 7 parameters,
> > got 0)
>
> This is because Affy changed the format of some of the data in the
> annotation .csv file. Benilton knows about this, and may have already
> put in the fix in the devel version.

Yes, I asked them to do that because you could not identify what
annotation data went with what enzyme (at least for fragment
information).  Background is the Affymetrix Forum thread
'Fragment-length data in the NetAffx CSV files for GenomeWideSNP_6?'
on Sept 19 2007, cf.

 https://www.affymetrix.com/community/forums/thread.jspa?threadID=4981&tstart=0

They solved the problem for GenomeWideSNP_6 and used the updated file
format for GenomeWideSNP_5.  However, the content in the
GenomeWideSNP_5 CSV file(s) is broken.  See thread 'Fragment-length
data in the NetAffx CSV files for GenomeWideSNP_5 (sic)?' on Dec 3
2007 for details:

 https://www.affymetrix.com/community/forums/thread.jspa?threadID=5341&tstart=0

There is no response from Affy.  In the mean time, in
aroma.affymetrix, I use GenomeWideSNP_6 annotation data instead after
some validity checks.  For details on the problem and the workaround
see aroma.affymetrix Page 'GenomeWideSNP_5 - Miscellaneous':

http://groups.google.com/group/aroma-affymetrix/web/genomewidesnp-5---miscellaneous

In summary, be careful when using the GenomeWideSNP_5 NetAffx annotation files.

/Henrik

>
> However, there are bigger problems than this. If you look at the example
> in ?AffySNPPDInfoPkgSeed-class, you will see that you need three other
> input files:
>
>       spline <- "pd.mapping250k.nsp.spline.params.rda"
>       refd <- "pd.mapping250k.nspRef.rda"
>       crlmmInf <- "pd.mapping250k.nspCrlmmInfo.rda"
>
> As far as I know these files have not been made for the SNP5.0 chips
> yet, and I don't think the package build will continue without them. I
> could be wrong on both counts, so those in the know should speak up if so.
>
> Best,
>
> Jim
>
>
>
> > In addition: Warning message:
> > ignoring zero-row bind.data in: sqliteExecStatement(conn, statement,
> > bind.data, ...)
> > Timing stopped at: 8.97 0.25 9.22 NA NA
> >
> >
> >
> >
> >
> >
> >
> >  sessionInfo()
> > R version 2.5.1 (2007-06-27)
> > i386-pc-mingw32
> >
> > locale:
> > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> > Kingdom.1252;LC_MONETARY=English_United
> > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
> >
> > attached base packages:
> > [1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
> > "datasets"  "methods"   "base"
> >
> > other attached packages:
> >         pdInfoBuilder                 oligo BufferedMatrixMethods
> > BufferedMatrix                affyio            affxparser
> > RSQLite                   DBI               Biobase
> >               "1.0.0"             "1.0.2-3"               "1.0.0"
> > "1.0.1"               "1.4.0"               "1.8.3"
> > "0.5-6"               "0.2-4"              "1.14.0"
> >
> >
> >
> >
> >
> >
> > ***********************************************
> > Sergii Ivakhno, PhD student
> > Computational Biology Group
> > Department of Oncology, University of Cambridge
> > Cancer Research UK Cambridge Research Institute
> > Li Ka Shing Centre
> > Robinson Way
> > Cambridge CB2 0RE
> > UNITED KINGDOM
> > Tel: +44 1223 404293
> > Fax: +44 1223 404208
> > E-mail: Sergii.Ivakhno at cancerresearchuk.org
> >
> > https://web.mit.edu/ivakhno/www/
> > ***********************************************
> >
> >
> >       [[alternative HTML version deleted]]
> >
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
>
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