[BioC] affy: CDF packages
Sundaram, Shyam (NIH/CIT)
shyam@mail.nih.gov
Thu, 21 Nov 2002 08:58:41 -0500
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Pawel:
You can actually load your own CDF file. There are two approaches to this.
(1) ReadAffy(CDFfile=NULL, CELfiles=NULL,widget=FALSE,
compress.cel=FALSE,compress.cdf=FALSE,
verbose=TRUE, chip.names=NULL,rm.mask=FALSE,
rm.outliers=FALSE,
rm.extra=FALSE, cdf.name = NULL, phenodata=NULL,
annotation="", description="", notes="", ...)
This will create the plob with the CDF object, CEL objects combined.
(2) read.cdffile(file, compress=TRUE)
This will allow you to read a cdf file alone and store as an cdf object.
Hope this helps.
Shyam
-----Original Message-----
From: Pawel Herzyk [mailto:ph53d@udcf.gla.ac.uk]
Sent: Thursday, November 21, 2002 8:29 AM
To: bioconductor
Subject: [BioC] affy: CDF packages
Dear CDF package maintainer,
It appeared to me that the web site for Affymetrix Data Packages does not
contain two packages corresponding to CDF files for two important chips
namely:
DrosGenome1.CDF - this is the current Drosophila chip
ATH1-121501.CDF - this is a new Arabidopsis Chip released earlier this year.
Also:
Is there any way that the user can use the actual CDF file or is he now
entirely dependent on the appropriate package being timely placed in the
bioconductor web-site?
regards
Pawel
-----------------------
Dr. Pawel Herzyk
p.herzyk@bio.gla.ac.uk <mailto:p.herzyk@bio.gla.ac.uk>
Head of Bioinformatics
0141-3303180
The Sir Henry Wellcome Functional Genomics Facility
Institute of Biomedical and Life Sciences
Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ
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<DIV><SPAN class=883193413-21112002><FONT face=Arial><FONT color=#0000ff><FONT
size=2>Pawel<SPAN
class=820095813-21112002>:</SPAN></FONT></FONT></FONT></SPAN></DIV>
<DIV><SPAN class=883193413-21112002><FONT face=Arial color=#0000ff size=2>You
can actually load your own CDF file. There are two approaches to this.
</FONT></SPAN></DIV>
<DIV><SPAN class=883193413-21112002><FONT face=Arial color=#0000ff
size=2>(1) </FONT></SPAN><SPAN class=883193413-21112002><FONT face=Arial
color=#0000ff size=2>ReadAffy(CDFfile=NULL,
CELfiles=NULL,widget=FALSE,<BR>
compress.cel=FALSE,compress.cdf=FALSE,<BR>
verbose=TRUE, chip.names=NULL,rm.mask=FALSE,
rm.outliers=FALSE,<BR>
rm.extra=FALSE, cdf.name = NULL,
phenodata=NULL,<BR>
annotation="", description="", notes="", ...)</FONT></SPAN></DIV>
<DIV><SPAN class=883193413-21112002><FONT face=Arial color=#0000ff size=2>
This will create the plob with the CDF object, CEL objects
combined.</FONT></SPAN></DIV>
<DIV><SPAN class=883193413-21112002><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=883193413-21112002><FONT face=Arial color=#0000ff size=2>(2)
read.cdffile(file, compress=TRUE)<BR> This will allow you to
read a cdf file alone and store as an cdf object.</FONT></SPAN></DIV>
<DIV><SPAN class=883193413-21112002><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=883193413-21112002><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=883193413-21112002><FONT face=Arial color=#0000ff size=2>Hope
this helps.</FONT></SPAN></DIV>
<DIV><SPAN class=883193413-21112002><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=883193413-21112002><FONT face=Arial color=#0000ff
size=2>Shyam</FONT></SPAN></DIV></DIV>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B> Pawel Herzyk
[mailto:ph53d@udcf.gla.ac.uk]<BR><B>Sent:</B> Thursday, November 21, 2002 8:29
AM<BR><B>To:</B> bioconductor<BR><B>Subject:</B> [BioC] affy: CDF
packages<BR><BR></FONT></DIV>
<DIV><FONT face=Arial size=2>Dear CDF package maintainer,</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>It appeared to me that the web site for
Affymetrix Data Packages does not contain two packages corresponding to CDF
files for two important chips namely:</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>DrosGenome1.CDF - this is the current Drosophila
chip</FONT></DIV>
<DIV><FONT face=Arial size=2>ATH1-121501.CDF - this is a new Arabidopsis Chip
released earlier this year.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>Also:</FONT></DIV>
<DIV><FONT face=Arial size=2>Is there any way that the user can use the actual
CDF file or is he now entirely dependent on the appropriate package being
timely placed in the bioconductor web-site?</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>regards</FONT></DIV>
<DIV><FONT face=Arial size=2>Pawel</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>-----------------------<BR>Dr. Pawel
Herzyk
<A href="mailto:p.herzyk@bio.gla.ac.uk">p.herzyk@bio.gla.ac.uk</A><BR>Head of
Bioinformatics
0141-3303180<BR>The Sir Henry Wellcome Functional Genomics
Facility<BR>Institute of Biomedical and Life Sciences<BR>Joseph Black
Building, University of Glasgow, Glasgow, G12 8QQ</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV></BLOCKQUOTE></BODY></HTML>
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