[BioC] error using pdInfoBuilder on Affymetrix snp 5.0 array

[Benilton Carvalho]

I'm creating the remaining metadata and fixing the code to accomodate  
these changes. Soon I'll have something in deve.

B

On Dec 13, 2007, at 10:28 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.
>
> 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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