[BioC] annaffy: YEAST vs. Affy YEAST_2 annotation

[Jacob Michaelson]

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