Hi, Agnes,
Thanks for your clear explanation!

Best,

Ren


-----Original Message-----
From: Paquet, Agnes [mailto:apaquet@medsfgh.ucsf.edu]
Sent: Fri 2/23/2007 2:34 PM
To: Na, Ren; bioconductor@stat.math.ethz.ch
Subject: RE: [BioC] question about the value retured by function ontoCompare()
 
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@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",endnode=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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