[BioC] GO from hu35ksuba

[James W. MacDonald]

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
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
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