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, 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. > > -- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 734-647-5623