[BioC] annaffy: YEAST vs. Affy YEAST_2 annotation

[Colin A. Smith]

Jacob-

The YEAST annotation package is a bit unlike all the others in that it 
does not include the "*SYMBOL" environment mapping probe set ids onto 
commonly used abbreviations for genes. In all the other annotation 
packages, using the "*SYMBOL" environment was an easy way to get a 
listing of every probe id on the chip. That doesn't work with the YEAST 
package. There will hopefully be an updated annaffy package which 
doesn't depend on the "*SYMBOL" environment for Probe searches in the 
next few days.

-Colin

On Feb 7, 2005, at 3:00, bioconductor-request at stat.math.ethz.ch wrote:

> Well, I've struggled quite a bit over the past several weeks to come up
> with a viable way to make an annaffy-compatible annotation package for
> the relatively new Affymetrix Yeast 2.0 chip.
>
> So far, in spite of everyone's generous help and tips, I haven't been
> successful.  I've gotten the closest to making it work by using
> yeastann and yeastPkgBuilder within AnnBuilder, but the data that's
> built just contains a bunch of "NA"s for everything but the probe ids
> and the SGD accession numbers (both of which I gave in the input file).
>   I'm unable to find the orf numbers required by yeastPkgBuilder, but I
> gave it a shot with the SGD accession numbers (which is really all I
> have to work with).  Obviously, it didn't work.
>
> Anyway, then I figured I might as well at least try to use the current
> YEAST annotation, to see how much of the Yeast 2.0 chip it covers.  I
> used aafSearchText (via annaffy in webbioc) to search for a list of
> probes from the Yeast 2.0 chip.  Here's the code and subsequent error
> message I got:
>> chip <- "YEAST"
>> colnames <- c("Probe")
>> text <- c("1769799_at
> + 1771363_at
> + 1779354_at
> + 1771073_at
> + 1770610_at
> + 1779591_at
> + 1779214_at
> + 1777292_at
> + 1779767_at
> + 1779046_at
> + 1777723_at")
>> library(annaffy)
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
> 	 Vignettes contain introductory material.  To view,
> 	 simply type: openVignette()
> 	 For details on reading vignettes, see
> 	 the openVignette help page.
> Loading required package: GO
> Loading required package: KEGG
> Loading required package: annotate
>> probeids <- aafSearchText(chip, colnames, text)
> Loading required package: YEAST
> Error in try(name) : Object "YEASTSYMBOL" not found
> Error in as.environment(pos) : no item called "YEASTSYMBOL" in the
> search list
> Execution halted
>
>
> This was also reproducible within the R console (Mac OS X 10.3.7).  I
> built the latest YEAST package from source, and could not find a
> "YEASTSYMBOL" component anywhere.
>
> I'm using R 2.0.1, with annaffy 1.0.11 and the latest YEAST package
> from the site.
>
> Any help?
>
> Thanks in advance,
>
> Jake Michaelson