[BioC] Finding Annotation of CEL file formats

cstrato cstrato at aon.at
Fri Sep 19 19:17:25 CEST 2008

Dear Gundula

If you have an Affymetrix CEL-file, e.g. Test3.CEL, you can do on Linux:
head -n17 Test3.CEL

For CEL-files of type text or xda you will see on line 15:
DatHeader=[12..40151]  Fetal 3:CLS=1167 RWS=1167 XIN=3  YIN=3  
VE=17        2.0 08/16/01 17:28:31       Test3.1sq                  6
This tells you that the CEL-file uses Test3.CDF as CDF file (Test3.1sq) 
and hybridized a "Fetal" tissue

For CEL-files of type Calvin you will see a  line:
affymetrix-dat-heade[6..38103]  Fetal 5:CLS=1167 RWS=1167 XIN=3  YIN=3  
VE=17        2.0 08/16/01 17:32:06       Test3.1sq                  6
This has the same information as above.

Then you can check on the Affymetrix web-site, for which organism the 
CDF-file was created:

Hope this information is helpful
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at

Gundala Viswanath wrote:
> Dear all,
> Given any CEL file, such as these:
> http://bioinf.boku.ac.at/pub/Chaix2008/CEL/supplCELdata.zip
> With BioConductor Is there a way we can find:
> 1. Which organism they come from?
> 2. Which organism's tissue they come from?
> 3. What are the probe names/gene name involved?
> I looked at "affy" package but I can't seem to find
> ways to get what I wanted above. But maybe I am wrong.
> - Gundala Viswanath
> Jakarta - Indonesia
> PS: Original URL for the data is this
> http://bioinf.boku.ac.at/pub/Chaix2008
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