[BioC] Re: Obtaining PM/MM data from .CEL files

[Stephen Nyangoma]

Hi Eric,
Thanks for the clear documentation of the commands that can lead to the
solution of my problem. 

Regards. Stephen.

On Mon, 2003-06-30 at 15:17, Eric wrote:Hi,

Rafael Irizarry was kind enough to walk me through this, and it worked
as of May of this year.
The text is here in the discussions thread
(https://www.stat.math.ethz.ch/pipermail/bioconductor/2003-April/001269.html)
Then you can use the write.table command to generate text files if you
want to export the values to other programs.

HTH,
-E



    When replying, please edit your Subject line so it is more specific
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    Today's Topics:
    
       1. obtaining PM/MM data from the .CEL files (Stephen Nyangoma)
       2. Re: obtaining PM/MM data from the .CEL files (James MacDonald)
    
    
    ----------------------------------------------------------------------
    
    Message: 1
    Date: 28 Jun 2003 12:49:25 +0200
    From: Stephen Nyangoma <S.Nyangoma at cs.rug.nl>
    Subject: [BioC] obtaining PM/MM data from the .CEL files
    To: bioconductor at stat.math.ethz.ch
    Message-ID: <1056797365.1728.6.camel at iwi142>
    Content-Type: text/plain
    
    
    
    Hi
    I am just beginning my research in the analysis of Oligonucleotide
    GeneChip data. I have difficulty getting information from the data
    bases. I have been given some .CEL files and I need to extract
    perfect
    match (PM)/mismatch (MM) pair signal intensities.
    
    Where can I get information how to do this? 
    Where can I get good information about extracting info from .CEL
    files? 
    
    Best regards.
    
    
    Stephen.
    
    
    ------------------------------
    
    Message: 2
    Date: Sat, 28 Jun 2003 11:28:35 -0400
    From: "James MacDonald" <jmacdon at med.umich.edu>
    Subject: Re: [BioC] obtaining PM/MM data from the .CEL files
    To: <S.Nyangoma at cs.rug.nl>, <bioconductor at stat.math.ethz.ch>
    Message-ID: <sefd7be6.035 at mail-01.med.umich.edu>
    Content-Type: text/plain; charset=US-ASCII
    
    You can get information from the help pages that come with R. Type
    help.start() to get a browser, and go to the affy help section.
    
    Additionally, you can get information from the vignettes that come
    with
    affy. You will find links to the vignettes at the top of the affy
    help
    page, or you can type openVignette() after library(affy) from within
    R.
    
    Jim
    
    James W. MacDonald
    UMCCC Microarray Core Facility
    1500 E. Medical Center Drive
    7410 CCGC
    Ann Arbor MI 48109
    734-647-5623
    
    >>> Stephen Nyangoma <S.Nyangoma at cs.rug.nl> 06/28/03 06:49AM >>>
    
    
    Hi
    I am just beginning my research in the analysis of Oligonucleotide
    GeneChip data. I have difficulty getting information from the data
    bases. I have been given some .CEL files and I need to extract
    perfect
    match (PM)/mismatch (MM) pair signal intensities.
    
    Where can I get information how to do this? 
    Where can I get good information about extracting info from .CEL
    files?
    
    
    Best regards.
    
    
    Stephen.
    
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    End of Bioconductor Digest, Vol 4, Issue 51
    *******************************************
Eric Blalock, PhD
Dept Pharmacology, UKMC
859 323-8033

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