Hi all,
I frequently use the Category package for geneset enrichment based on GO
terms. My GO annotation information often comes from biomaRt or other
sources and not directly from the GO package, so now and then I run into
version conflicts when a given GO term is not or no longer included in
the GO package. The cateGOry function used to stop with an error message
listing the unknown GO terms, but in one of the later versions this
changed to a list of indices into the vector of GO terms. Now the
problem is that these indices do not match the originial imput vector
(some remodeling goes on in the augmentByAncestorsSmart function, I
think. So in order to identify the missing GO terms I have to debug and
dig deep into the guts of augmentByAncestors. Wouldn't it be possible to
report the missing GO terms via the GO identifier (as it was before) so
I can easily remove them from my analysis. Or should this be done by the
function with a warning?
Cheers,
Florian
R version 2.5.0 Under development (unstable) (2007-01-24 r40564)
i686-pc-linux-gnu
locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
attached base packages:
[1] "splines" "grid" "tools" "stats" "graphics" "grDevices"
[7] "datasets" "utils" "methods" "base"
other attached packages:
GOstats RBGL biomaRt RCurl XML
rnaiUtils
"2.2.1" "1.11.4" "1.10.0" "0.8-0" "1.4-1"
"1.0"
Category Matrix lattice annotate GO
KEGG
"2.2.2" "0.9975-11" "0.14-16" "1.14.1" "1.16.0"
"1.15.12"
graph cellHTS genefilter survival prada
RColorBrewer
"1.14.0" "1.5.9" "1.13.8" "2.30" "1.12.0"
"0.2-3"
Biobase
"1.13.39"