[BioC] Sc03b_MR_v04 CDF package
Ludo Muller
ludo.muller at duke.edu
Wed Aug 27 21:34:50 CEST 2008
James, you are right about the erroneous bpmap files. I contacted
Affymetrix about this problem and after looking into it, they confirmed
that a lot of the mm probes have the same coordinates as the pm probes in
the bpmap files. They are supposedly working to fix the problem, but
couldn't give me an estimate of when they would have a corrected bpmap
file.
Do you know if it is possible to extract just the pm hybridization
intensity values from the cel files without a corrected bpmap file? I don't
necessarily need the mm probe intensity values since there are alternative
ways for background correction that don't rely on them.
Thanks again,
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: 08/22/2008 08:00AM
cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Sc03b_MR_v04 CDF package
So I tracked this down, and it _doesn't_ appear to be a bug in
pdInfoBuilder. It appears to be either an error or an inconsistency in
the Affy bpmap files. I didn't use the yeast chip, as I am not sure I
can get the one you used but I get the same error with the Arabidopsis
bpmap so I used that one.
It all boils down to this:
> library(affxparser)
> tmp <- readBpmap("At35b_MF_v04-2_TIGRv5.bpmap", 26)
> head(do.call("cbind",tmp[[1]][2:5]), n=20)
pmx pmy mmx mmy
[1,] 2197 2194 2198 2194
[2,] 2379 997 2380 997
[3,] 2443 1111 2444 1111
[4,] 2485 826 2486 826
[5,] 2491 2374 2492 2374
[6,] 2497 826 2498 826
[7,] 2503 1602 2504 1602
[8,] 2505 1129 2506 1129
[9,] 2507 2022 2508 2022
[10,] 1687 169 1688 169
[11,] 1687 501 1688 501
[12,] 1687 638 1688 638
[13,] 1687 871 1688 871
[14,] 1687 873 1688 873
[15,] 1687 1007 1688 1007
[16,] 1687 1371 1688 1371
[17,] 1687 1492 1688 1492
[18,] 1687 2346 1688 2346 <-
[19,] 1687 2347 1688 2346 <-
[20,] 1689 287 1690 287
As you can see, for this QC probeset there are two MM probes that appear
to be right on top of each other. I assume the second should really have
an (1688, 2347) coordinate, but the bpmap is in error. Since this will
make two identical indices which are used as the primary key for the
table these data are being fed into we get an error as the primary key
must be unique.
For the A. thaliana chip there are 36 such errors in the bpmap file for
just the QC probes.
Best,
Jim
Ludo Muller wrote:
> 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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Hildebrandt Lab
> 8220D MSRB III
> 1150 W. Medical Center Drive
> Ann Arbor MI 48109-0646
> 734-936-8662
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662
More information about the Bioconductor
mailing list