[BioC] Sc03b_MR_v04 CDF package

[Ludo Muller]

Hi James,

Thank you for your help. I installed the pdInfoBuilder package locally, on
my Win XP computer (I also requested it to be installed on a Linux server,
in case my computer doesn't have enough memory), and I ran the following (I
downloaded the appropriate .bpmap and .cif files):

> pkg <- new("AffyTilingPDInfoPkgSeed",version="0.0.1",author="Ludo
Muller",email="ludo.muller
at ...",biocViews="AnnotationData",genomebuild="Stanford Yeast Genome
Database, October
2003",bpmapFile="Sc03b_MR_v04.bpmap",cifFile="Sc03b_MR_v04.cif")
> makePdInfoPackage(pkg,destDir=".")

However, I get the following message:

Creating package in ./pd.sc03b.mr.v04
Error in sqliteExecStatement(conn, statement, bind.data, ...) :
  RS-DBI driver: (RS_SQLite_exec: could not execute: PRIMARY KEY must be
unique)
Timing stopped at: 6.35 0.17 6.59

I found an earlier report dealing with a similar error message:
https://stat.ethz.ch/pipermail/bioconductor/2008-June/023080.html

Is it likely that the information files for this array are also inaccurate?

Cheers,

Ludo.

---
Ludo A.H. Muller, Ph.D.
Dept. of Molecular Genetics & Microbiology
Box 3020, Duke University Medical Center
Durham, NC 27710, USA

Phone: +1 (919) 681-6781 or 681-6778
Fax: +1 (919) 684-8735
E-mail: ludo.muller at duke.edu
Homepage: http://www.duke.edu/~mulle019



-----"James W. MacDonald" <jmacdon at med.umich.edu> wrote: -----


To: Ludo Muller <ludo.muller at duke.edu>
From: "James W. MacDonald" <jmacdon at med.umich.edu>
Date: 08/19/2008 09:05AM
cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Sc03b_MR_v04 CDF package

Hi Ludo,

Ludo Muller wrote:
> Hi all,
>
> I have data from hybridizations onto the Affymetrix yeast tiling array
> (Sc03b_MR_v04) which I would like to analyze using Bioconductor. However
> the CDF package (sc03bmrv04cdf) for this array doesn't seem to be
available
> from the bioconductor website. Can anybody tell me if it is available
> elsewhere or whom I could contact about creating this package?

There will probably never be such a beast, as that implies the usage of
the affy package. Instead, you should be using the oligo package and
pdInfoBuilder. For that you will need the CIF and BPMAP files from Affy,
and something like

pkg <- new("AffyTilingPDInfoPkgSeed", version = "0.0.1", author = "You",
email = "you at yours.com", biocViews = "AnnotationData", genomebuild =
"thegenomebuild", bpmapFile = <name of bpmap file>, cifFile = <name of
cif file>)

makePdInfoPackage(pkg)

And then install using R CMD INSTALL <the package name>. You don't
mention your OS, so that might simply entail running the above at a
terminal prompt (if on Linux), or if you are on Windows or MacOS, you
will need to get set up to build packages. See the R FAQ for either OS
for further info about that.

Best,

Jim


>
> Cheers,
>
> Ludo.
>
> ---
> Ludo A.H. Muller, Ph.D.
> Dept. of Molecular Genetics & Microbiology
> Box 3020, Duke University Medical Center
> Durham, NC 27710, USA
>
> Phone: +1 (919) 681-6781 or 681-6778
> Fax: +1 (919) 684-8735
> E-mail: ludo.muller at duke.edu
> Homepage: http://www.duke.edu/~mulle019
>
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--
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662