[BioC] GO from hu35ksuba

[Adaikalavan Ramasamy]

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_annot_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
> 
>