[BioC] filtering in GSEABase package

[Jason Lu]

Hi All,

I noticed a problem which I am not sure if I miss something.

I attempt to select GO terms in the biological process categories
(BP). But for some reasons the filtering seems not working. One id is
in the MF category, but still is selected (see below).


 library(GSEABase)
 data(sample.ExpressionSet)
 gg <- GeneSetCollection(sample.ExpressionSet[200:250],
                                      setType = GOCollection(ontology="BP"))

goId = "GO:0003676"  # is in MF, not in BP

goId %in% names(gg)
TRUE

> sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-redhat-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] hgu95av2.db_2.3.5   org.Hs.eg.db_2.3.6  KEGG.db_2.3.5
 [4] Category_2.12.0     GO.db_2.3.5         GSEABase_1.8.0
 [7] graph_1.24.1        annotate_1.24.0     mouse4302.db_2.3.5
[10] org.Mm.eg.db_2.3.6  RSQLite_0.7-3       DBI_0.2-5
[13] AnnotationDbi_1.8.1 genefilter_1.28.2   ALL_1.4.7
[16] Biobase_2.6.1

loaded via a namespace (and not attached):
[1] RBGL_1.22.0     splines_2.10.0  survival_2.35-7 tools_2.10.0
[5] XML_2.6-0       xtable_1.5-6
>

Thanks for looking into this.

Jason