[BioC] ontoCompare - 1) notFound 2) GO level

[Paquet, Agnes]

Hi Michaela,
 
You can generate a different endnode list using the function CustomEndNodeList:
 
MFendnode <- CustomEndNodeList("GO:0003674", rank=3)
ontoCompare(affylist, probeType="hgu133a", endnode=MFendnode, goType="MF")

You can also select endnodes of interest for your project using a GEO browser like Amigo and pass the vector of corresponding GO ids as endnode.
 
Best,
 
Agnes

 

________________________________

From: bioconductor-bounces at stat.math.ethz.ch on behalf of Michaela Gündel
Sent: Wed 8/29/2007 8:20 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] ontoCompare - 1) notFound 2) GO level



Dear list,

after downloading data from GEO (which is already GO id annotated) I do a GO
analysis using ontoCompare. It all works fine, but the thing I don't
understand is why there are so many (around 40%) notFounds. Is the mapping
old or how can this happen? I don't believe the GO identifiers are faulty
because they come from GEO.

Another question is how to limit the GO terms that are output to a certain
GO level, eg. 3, because the high-level terms are not very informative. Is
it possible to do this in some way, maybe using the endnodelist?

Thank you very much in advance, any help is appreciated!!

Michaela Guendel

R version 2.5.1 (2007-06-27)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "methods"   "base"

other attached packages:
  GEOquery    goTools         GO     RMySQL        DBI    biomaRt      RCurl
   "2.0.5"    "1.8.0"   "1.16.0"    "0.6-0"    "0.2-3"   "1.10.1"    "0.6-0"
       XML  hgug4112a   annotate      Cairo genefilter   survival    Biobase
   "1.9-0"   "1.16.0"   "1.14.1"    "1.3-5"   "1.14.1"     "2.32"   "1.14.0"
     limma
  "2.10.5"

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