[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)&nbsp; </FONT></SPAN><SPAN class=883193413-21112002><FONT face=Arial 
color=#0000ff size=2>ReadAffy(CDFfile=NULL, 
CELfiles=NULL,widget=FALSE,<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
compress.cel=FALSE,compress.cdf=FALSE,<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
verbose=TRUE, chip.names=NULL,rm.mask=FALSE, 
rm.outliers=FALSE,<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
rm.extra=FALSE, cdf.name = NULL,&nbsp; 
phenodata=NULL,<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
annotation="", description="", notes="", ...)</FONT></SPAN></DIV>
<DIV><SPAN class=883193413-21112002><FONT face=Arial color=#0000ff size=2>&nbsp; 
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>&nbsp;</DIV>
<DIV><SPAN class=883193413-21112002><FONT face=Arial color=#0000ff size=2>(2) 
read.cdffile(file, compress=TRUE)<BR>&nbsp;&nbsp;&nbsp; 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>&nbsp;</DIV>
<DIV><SPAN class=883193413-21112002><FONT face=Arial color=#0000ff 
size=2></FONT></SPAN>&nbsp;</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>&nbsp;</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>&nbsp;</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>&nbsp;</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>&nbsp;</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>&nbsp;</DIV>
  <DIV><FONT face=Arial size=2>regards</FONT></DIV>
  <DIV><FONT face=Arial size=2>Pawel</FONT></DIV>
  <DIV>&nbsp;</DIV>
  <DIV><FONT face=Arial size=2>-----------------------<BR>Dr. Pawel 
  Herzyk&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
  <A href="mailto:p.herzyk@bio.gla.ac.uk">p.herzyk@bio.gla.ac.uk</A><BR>Head of 
  Bioinformatics&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
  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>&nbsp;</DIV>
  <DIV><FONT face=Arial size=2></FONT>&nbsp;</DIV></BLOCKQUOTE></BODY></HTML>

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