<html>
Hi,<br><br>
Rafael Irizarry was kind enough to walk me through this, and it worked as
of May of this year.<br>
The text is here in the discussions thread
(<a href="https://www.stat.math.ethz.ch/pipermail/bioconductor/2003-April/001269.html" eudora="autourl">https://www.stat.math.ethz.ch/pipermail/bioconductor/2003-April/001269.html</a>)<br>
Then you can use the write.table command to generate text files if you
want to export the values to other programs.<br><br>
HTH,<br>
-E<br><br>
<br>
<blockquote type=cite class=cite cite>When replying, please edit your
Subject line so it is more specific<br>
than "Re: Contents of Bioconductor digest..."<br><br>
<br>
Today's Topics:<br><br>
1. obtaining PM/MM data from the .CEL files (Stephen
Nyangoma)<br>
2. Re: obtaining PM/MM data from the .CEL files (James
MacDonald)<br><br>
<br>
----------------------------------------------------------------------<br><br>
Message: 1<br>
Date: 28 Jun 2003 12:49:25 +0200<br>
From: Stephen Nyangoma <S.Nyangoma@cs.rug.nl><br>
Subject: [BioC] obtaining PM/MM data from the .CEL files<br>
To: bioconductor@stat.math.ethz.ch<br>
Message-ID: <1056797365.1728.6.camel@iwi142><br>
Content-Type: text/plain<br><br>
<br><br>
Hi<br>
I am just beginning my research in the analysis of Oligonucleotide<br>
GeneChip data. I have difficulty getting information from the data<br>
bases. I have been given some .CEL files and I need to extract
perfect<br>
match (PM)/mismatch (MM) pair signal intensities.<br><br>
Where can I get information how to do this? <br>
Where can I get good information about extracting info from .CEL files?
<br><br>
Best regards.<br><br>
<br>
Stephen.<br><br>
<br>
------------------------------<br><br>
Message: 2<br>
Date: Sat, 28 Jun 2003 11:28:35 -0400<br>
From: "James MacDonald" <jmacdon@med.umich.edu><br>
Subject: Re: [BioC] obtaining PM/MM data from the .CEL files<br>
To: <S.Nyangoma@cs.rug.nl>,
<bioconductor@stat.math.ethz.ch><br>
Message-ID: <sefd7be6.035@mail-01.med.umich.edu><br>
Content-Type: text/plain; charset=US-ASCII<br><br>
You can get information from the help pages that come with R. Type<br>
help.start() to get a browser, and go to the affy help section.<br><br>
Additionally, you can get information from the vignettes that come
with<br>
affy. You will find links to the vignettes at the top of the affy
help<br>
page, or you can type openVignette() after library(affy) from within
R.<br><br>
Jim<br><br>
James W. MacDonald<br>
UMCCC Microarray Core Facility<br>
1500 E. Medical Center Drive<br>
7410 CCGC<br>
Ann Arbor MI 48109<br>
734-647-5623<br><br>
>>> Stephen Nyangoma <S.Nyangoma@cs.rug.nl> 06/28/03
06:49AM >>><br><br>
<br>
Hi<br>
I am just beginning my research in the analysis of Oligonucleotide<br>
GeneChip data. I have difficulty getting information from the data<br>
bases. I have been given some .CEL files and I need to extract
perfect<br>
match (PM)/mismatch (MM) pair signal intensities.<br><br>
Where can I get information how to do this? <br>
Where can I get good information about extracting info from .CEL
files?<br><br>
<br>
Best regards.<br><br>
<br>
Stephen.<br><br>
_______________________________________________<br>
Bioconductor mailing list<br>
Bioconductor@stat.math.ethz.ch <br>
<a href="https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor" eudora="autourl">https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor</a><br><br>
<br>
------------------------------<br><br>
_______________________________________________<br>
Bioconductor mailing list<br>
Bioconductor@stat.math.ethz.ch<br>
<a href="https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor" eudora="autourl">https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor</a><br>
<br><br>
End of Bioconductor Digest, Vol 4, Issue 51<br>
*******************************************</blockquote>
<x-sigsep><p></x-sigsep>
Eric Blalock, PhD<br>
Dept Pharmacology, UKMC<br>
859 323-8033<br><br>
<font size=1><u>STATEMENT OF CONFIDENTIALITY<br><br>
</u></font><font size=1 color="#333333">The contents of this e-mail
message and any attachments are confidential and are intended solely for
addressee. The information may also be legally privileged. This
transmission is sent in trust, for the sole purpose of delivery to the
intended recipient. If you have received this transmission in error, any
use, reproduction or dissemination of this transmission is strictly
prohibited. If you are not the intended recipient, please immediately
notify the sender by reply e-mail or at (859) 323-8033 and delete this
message and its attachments, if any.</font></html>