Yes, you are right. I was confusing building meta packages with building CDFs. Thank you for the explanation. Also thanks to Jeff Gentry (and indirectly to Jianhua Zhang) for providing me the R package in an offline mail saving me the trouble of trying to build it from scratch. Regards, Adai On Tue, 2005-06-21 at 09:09 -0400, James W. MacDonald wrote: > Adaikalavan Ramasamy wrote: > > Sorry if this question is documented somewhere but I could not find the > > answer to it. Feel free to point this out to me ? > > > > I am trying to get some gene ontology info from the chip Hu35KsubA for > > which I think I need the package "hu35ksuba". Note that this is not the > > same as "hu35ksubacdf" which is already provided by BioConductor. > > > > 1) Am I correct in thinking that I need "hu35ksuba" only ? > > > > 2) I do not think someone has built this for R. Can I download the CDF > > file and then use make.cdf.env() to do this ? If anyone has this and is > > willing to share, please send them to me offline and I would be very > > grateful. > > You are confused; make.cdf.env() makes the environment for the > hu35ksubacdf package, not the annotation package. > > > > > 3) Where do I get the CDF file from ? I cannot see it on this site > > http://www.affymetrix.com/support/technical/byproduct.affx?product =hu35k > > As noted, you don't need the CDF file (which simply maps chip > coordinates to probes). > > You will need to use the ABPkgBuilder() function in AnnBuilder. For this > you will need a text file containing a column of Affy IDs and a column > of Entrez Gene IDs, which you can get from this file: > > http://www.affymetrix.com/Auth/analysis/downloads/taf/Hu35KsubA_anno t_csv.zip > > I think the vignette for this package is relatively straightforward. See > ABPrimer for more info. > > Best, > > Jim > > > > > Thank you. > > > > Regards, Adai > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > >