[BioC] error using pdInfoBuilder on Affymetrix snp 5.0 array

[James W. MacDonald]

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/  
> ***********************************************
> 
> 
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> 
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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