[BioC] problem with annaffy aafFunction function

[James W. MacDonald]

Kimpel, Mark William wrote:
> I am using annaffy to annotate some rat data. When using the aafFunction
> in affaffy, all of the objects returned were "character(0)". I then
> tried the function using the example code from the help page. I was
> surprised to get the same result. Is there a problem here? Session info,
> example code, and results below. Thanks. Mark

Looks like you are getting what you should be.

 From ?aafFunction

Value:

      An 'aafList' of 'aafFunction' objects. NA values are returned as
      empty objects.


 > hgu95av2()


Quality control information for  hgu95av2
Date built: Created: Tue Aug 30 19:13:25 2005

Number of probes: 12625
Probe number missmatch: None
Probe missmatch: None
Mappings found for probe based rda files:
	 hgu95av2ACCNUM found 12625 of 12625
	 hgu95av2CHRLOC found 11764 of 12625
	 hgu95av2CHR found 12266 of 12625
	 hgu95av2ENZYME found 1895 of 12625
	 hgu95av2GENENAME found 11506 of 12625
	 hgu95av2GO found 11319 of 12625
	 hgu95av2LOCUSID found 12337 of 12625
	 hgu95av2MAP found 12224 of 12625
	 hgu95av2OMIM found 9972 of 12625
	 hgu95av2PATH found 3843 of 12625
	 hgu95av2PMID found 12203 of 12625
	 hgu95av2REFSEQ found 12114 of 12625
	 hgu95av2SUMFUNC found 0 of 12625
	 hgu95av2SYMBOL found 12280 of 12625
	 hgu95av2UNIGENE found 12225 of 12625
Mappings found for non-probe based rda files:
  	 hgu95av2CHRLENGTHS found 25
	 hgu95av2ENZYME2PROBE found 632
	 hgu95av2GO2ALLPROBES found 5574
	 hgu95av2GO2PROBE found 4011
	 hgu95av2ORGANISM found 1
	 hgu95av2PATH2PROBE found 151
	 hgu95av2PMID2PROBE found 96685

Note that there are zero mappings for hguav2SUMFUNC, hence all should be NA.

Best,

Jim


> 
> sessionInfo:
> 
> R version 2.2.0, 2005-10-06, i386-pc-mingw32 
> 
> attached base packages:
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
> "datasets"  "base"     
> 
> other attached packages:
>   hgu95av2   annotate    rat2302 reposTools       affy    annaffy
> KEGG         GO    Biobase    RWinEdt 
>   "1.10.0"    "1.8.0"    "1.8.5"    "1.8.0"    "1.8.1"    "1.2.0"
> "1.8.1"    "1.6.5"    "1.8.0"    "1.7-3"
> 
> Example code used:
> 
> if (require(hgu95av2)) {
>          data(aafExpr)
>          probes <- geneNames(aafExpr)
>          functions <- aafFunction(probes, "hgu95av2")
>          show(functions[6:10])
>      }
> 
> Results:
> 
> An object of class "aafList"
> [[1]]
> An object of class "aafFunction"
> character(0)
> 
> [[2]]
> An object of class "aafFunction"
> character(0)
> 
> [[3]]
> An object of class "aafFunction"
> character(0)
> 
> [[4]]
> An object of class "aafFunction"
> character(0)
> 
> [[5]]
> An object of class "aafFunction"
> character(0)
> 
> Mark W. Kimpel MD 
> 
>  
> 
> Official Business Address:
> 
>  
> 
> Department of Psychiatry
> 
> Indiana University School of Medicine
> 
> Biotechnology, Research, & Training Center
> 
> 1345 W. 16th Street
> 
> Indianapolis, IN  46202
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor


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