[BioC] Problem with obtaining annotation of mgu74av2 chip

Richard Friedman friedman at cancercenter.columbia.edu
Mon May 31 21:55:45 CEST 2004

Dear Bioconductor users,

	I am trying to use annotate and annaffy to write the annotation of
the mgu74av2 chip to a text file which can be read with an Excel 
I am able to write all of the datatypes that are listed in response to 
the command
aaf.handler() with the exception of Gene Ontology and Pathway.
A record of my commands follows:

 > library("annotate")
 > library("mgu74av2")
 > ls("package:mgu74av2")
  [1] "mgu74av2"             "mgu74av2ACCNUM"       "mgu74av2CHR"        
   "mgu74av2CHRLENGTHS"   "mgu74av2CHRLOC"
  [6] "mgu74av2ENZYME"       "mgu74av2ENZYME2PROBE" "mgu74av2GENENAME"   
   "mgu74av2GO"           "mgu74av2GO2ALLPROBES"
[11] "mgu74av2GO2PROBE"     "mgu74av2GRIF"         "mgu74av2HGID"       
   "mgu74av2LOCUSID"      "mgu74av2MAP"
[16] "mgu74av2NM"           "mgu74av2NP"           "mgu74av2OMIM"       
   "mgu74av2ORGANISM"     "mgu74av2PATH"
[21] "mgu74av2PATH2PROBE"   "mgu74av2PMID"         "mgu74av2PMID2PROBE" 
   "mgu74av2QC"           "mgu74av2SUMFUNC"
[26] "mgu74av2SYMBOL"       "mgu74av2UNIGENE"

 > mgu74av2()

Quality control information for  mgu74av2
Date built:  Thu Mar  4 10:56:19 2004
Number of probes: 12488
Probe number missmatch: None
Probe missmatch: None
Mappings found for probe based rda files:
	 mgu74av2ACCNUM found 12488 of 12488
	 mgu74av2CHRLOC found 10347 of 12488
	 mgu74av2CHR found 11762 of 12488
	 mgu74av2ENZYME found 1028 of 12488
	 mgu74av2GENENAME found 11806 of 12488
	 mgu74av2GO found 9305 of 12488
	 mgu74av2GRIF found 4261 of 12488
	 mgu74av2HGID found 10202 of 12488
	 mgu74av2LOCUSID found 12196 of 12488
	 mgu74av2MAP found 11459 of 12488
	 mgu74av2NM found 10319 of 12488
	 mgu74av2NP found 10319 of 12488
	 mgu74av2OMIM found 1 of 12488
	 mgu74av2PATH found 1384 of 12488
	 mgu74av2PMID found 11348 of 12488
	 mgu74av2SUMFUNC found 1 of 12488
	 mgu74av2SYMBOL found 11806 of 12488
	 mgu74av2UNIGENE found 11336 of 12488
Mappings found for non-probe based rda files:
  	 mgu74av2ENZYME2PROBE found 390
	 mgu74av2GO2ALLPROBES found 3907
	 mgu74av2GO2PROBE found 2834
	 mgu74av2PATH2PROBE found 116
	 mgu74av2PMID2PROBE found 20782
 > anncols <-aaf.handler()[c(1:13)]
 > probeids <-ls(mgu74av2SYMBOL)
 > symbols <- aafSymbol(probeids,"mgu74av2")
 > ls()
[1] "anncols"      "last.warning" "probeids"     "symbols"
 > anntable<- aafTableAnn(probeids[1:12488],"mgu74av2",anncols)
Error in exists(num$GOID, GOTERM) : Object "GOTERM" not found
 > ls()
[1] "anncols"      "last.warning" "probeids"     "symbols"

However, when I try

 > anncols <-aaf.handler()[c(1:11)]
 > ls()
[1] "anncols"      "gbs"          "last.warning" "mgu74av2cdf"  
"probeids"     "symbols"
 > anntable<- aafTableAnn(probeids[1:12488],"mgu74av2",anncols)
 > ls()
[1] "anncols"      "anntable"     "gbs"          "last.warning" 
"mgu74av2cdf"  "probeids"     "symbols"
 > saveText(anntable,"mgu74av2.c1-11.txt")

The above commands completed without error and can be read with a file 
that I can read with an Excel Spreadsheet.

I would very much like to have the Gene Ontology and Pathway annotation.
I would appreciate any suggestions by which I could obtain it with this 
program or
any other programs.

Thanks and best wishes,
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu

"I'm giving up coffee. Now that it looks like I might top
6 feet, I don't want to risk spoiling it."
- Isaac Friedman, age 14
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