[BioC] usage of "all" category in annotation data

[James W. MacDonald]

Hi Michael,

Michael Newton wrote:
> 
> I'm seeking advice on the use of the "all" component in various
> annotation data packages relative to GO.
> 
> Using R version 2.4.1 and (e.g.) hgu133plus version 1.14.0,
> 
> library(hgu133plus2)   ## an Affy data package
> x <- as.list( hgu133plus2GO2ALLPROBES )  ##probe sets for each GO term
> 
> xa <- unique( x[["all"]] )    ## holds probe sets associated to "all"
> 
> xbp <- unique( x[["GO:0008150"]] )    # biological process
> xmf <- unique( x[["GO:0003674"]] )    # molecular function
> xcc <- unique( x[["GO:0005575"]] )    # cellular component
> 
> ## note that the following is true
> 
> all( xa == xbp )
> 
> But further checks show that the molecular function probe sets are not
> a subset of "all".

Note that the 'all' term no longer exists AFAICT in the current versions 
of annotation packages. I wasn't in on the discussion (if any) that 
resulted in this being removed, but I would imagine the rationale would 
have been that the 'all' term is a trivial result and can be extracted 
easily enough without having an explicit term.

Best,

Jim


> 
> I was under the impression that "all" is the union of MF, BP, and CC,
> but in the few libraries I've checked, "all" equals BP.  I haven't
> found a discussion of the matter in the few vignettes that might be
> relevant.
> 
> Is "all" really "BP", or is it supposed to be the union?
> 
> thanks,
> 
> -Michael N.
> 
> --
> 
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-- 
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
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