[BioC] "all" category in annotation data

[Marc Carlson]

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".
>
> 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.
>
>   
Hi Michael,

The difference between go_bp_all and go_bp is that "go_bp_all" ALSO
contains the go terms that are the parent terms to the most specific
terms.  It helps to know that GO ontologies are directed acyclic graphs,
and therefore anything beyond the specific term is probably redundant
information.  Therefore, the "go_bp_all" environment is really just
included here for convenience.


As for your code, I tried running it and noticed the following:

The expression:

xa <- unique( x[["all"]] )

This just assigns a null value to xa.  I am pretty sure that this is not
what you had in mind.  I assume this is a consequence of what James just
wrote in about "all".


And so then when you say:

all( xa == xbp )

what happens here is that you get true returned just because the null
value is considered to be true.  In other words if you say all(xa) or
all(NULL) you also get TRUE returned.


    Hope this helps you,

        Marc