[Bioc-devel] Annotation: hgfocus missing

[James W. MacDonald]

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

source("http://www.bioconductor.org/biocLite.R")
biocLite("hgfocus")

and then try the annaffy code again.

As an aside, the Bioc-devel list is intended for discussions pertaining 
to the development of packages and other 'higher level' discussions. 
General help questions should be directed to the regular BioC listserv 
at bioconductor at stat.math.ethz.ch.

Best,

Jim


> 
> 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
> 
> _______________________________________________ 
> Bioc-devel at stat.math.ethz.ch mailing list 
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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