[Bioc-devel] Annotation: hgfocus missing

James W. MacDonald jmacdon at med.umich.edu
Thu Mar 23 18:13:13 CET 2006

abprog at charter.net wrote:
> Hi, I am working on a group of microarrays that are publicly
> available. They are an affybach object. When I type the name of the
> object it reports that they are annotated: annotation=hgfocus There
> are other ways to find the annotation of the probesets which I have
> already done, but I wanted to test a paper in the bioconductor home
> page that was recommending to use annaffy package. Following the
> instructions here is what I get:
>> gbs<-aafGenBank(probeids,"hgfocus")
> [1] "You are missing hgfocus looking to see if it is available." 
> Error in chkPkgs(chip) : couldn't find function "userQuery"

Looks like a bug in chkPkgs(). Anyway, the fix is simple enough. Either 
load the ReposTools package first, or do


and then try the annaffy code again.

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> I do not see a package "chip" in the libraries I have downloaded, and
> the same in the list online: 
> http://www.bioconductor.org/packages/bioc/1.8/ Is there a place where
> I can download hgfocus? I tried with affymetrix homepage, but it
> creates a large group of files and at the end the setup aborts
> because it wants in our computers to have SQL server, which is
> nonsense.
> Thank you in advance for any suggestions, AB
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James W. MacDonald, M.S.
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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