Entering edit mode
jason0701
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190
@jason0701-3921
Last seen 5.1 years ago
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