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Paquet, Agnes
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@paquet-agnes-807
Last seen 9.9 years ago

Hi Ren,
GoTools provides 3 ways to count the number of children for each
endnode. I will use the Affymetrix data example affylist provided in
the package to illustrate the methods. This data object contains 3
sets of ids from Affymetrix hgu133a.
"None": for each ennode, return the number of children for this node.
For example, if you run ontoCompare on the example data:
ontoCompare(affylist,probeType="hgu133a",method="none",goType="BP")
The node cellular process gets the following hits:
L1 L2 L3
64 64 52
Since the total number of children is dependant on how many oligos you
are providing in your vector, or on how well these oligos are
annotated, some people prefer to look at a proportion rather than a
total count. GoTools provides the other methods for this purpose:
TGENES: for each endnode, return number of children for this node /
number of oligo (genes) in the group of oligos you provide:
ontoCompare(affylist,probeType="hgu133a",method="TGenes",goType="BP")
Example for affylist: number of oligo ids in the list is
L1 L2 L3
100 90 70
So the final result for the node Cellular Process in this case is:
L1: 64/100=0.64
L2: 64/90 = 0.71
L3: 52/70 = 0.74
TIDS: for each endnode, return number of children of this node / total
number of GO ids describing the group of oligos you provide.
ontoCompare(affylist,probeType="hgu133a",method="TIDS",goType="BP")
The number of GO ids for affylist is:
L1 L2 L3
388 379 334
(these are calculated internaly by ontoCompare, please refer to the
code for more details)
In this case, the results for the node Cellular process are:
L1: 64/388 = 0.164
L2: 64/379 = 0.169
L3: 52/ 334 = 0.17
I hope these examples will help you understand how goTools works.
Please don't hesitate to email me again if you have other questions.
Best,
Agnes
________________________________
From: bioconductor-bounces@stat.math.ethz.ch on behalf of Na, Ren
Sent: Thu 2/22/2007 12:36 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] question about the value retured by function
ontoCompare()
Hi,
I tried to use function ontoCompare() in package goTool.
myontoCompare<-ontoCompare(mylist,probeType="hgu133a",goType="BP",endn
ode=myendnode,method="TGenes",plot=TRUE)
I got bar chart. I am wondering whether the height of the bar is the
number of probes which belong to the corresponding GO term(end node)
devided by the total number of probe ids in one of the two lists. But
from the document "goTools.pdf", it says "TGenes: for each end node,
return the number of direct children found/ total number of probe
ids". I am not very clear about this part. Could someone help me here?
Thanks!
Ren
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