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

Hi Gundala, 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? The only information you can glean from the celfile will be particular to the celfile itself. So you can determine that they are hgu133plus2 chips, but I don't think you can determine the organism. Of course you could just download the target description file and use that: http://bioinf.boku.ac.at/pub/Chaix2008/target_info.txt > 2. Which organism's tissue they come from? Again, probably not. > 3. What are the probe names/gene name involved? The easiest way would be to use the hgu133plus2.db package. Best, Jim > > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662

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: http://www.affymetrix.com/support/technical/byproduct.affx?cat=exparra ys Hope this information is helpful Regards Christian _._._._._._._._._._._._._._._._._._ 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >