Hi all,

I am using ontoCompare to produce graphics for some experiments. The
datasets

are Agilent microarray based. So i have mapped all of the IDs to GO terms
and i

feed GO terms from differentially expressed lists as an input into goTools.
The

aim then is to see how these fall into higher GO categories and draw a plot.


Often, it is a comparison of upregulated vs downregulated genelists for any

given experiment.



The scientists that i work with often have a few functional categories that

they would like their differentially expressed genes to turn up in and this
was

one of the reasons i started to use goTools as it had an option for passing
in

customised endnode lists. But so far, i haven't had this bit work
successfully

on my data.

Version: I am using R 2.4.1 and goTools 1.6.0 method = 'TIDS'

1. I have used the MFnode <- CustonEndNodeList("GO:0003674", rank = 2)

declaration and though this works fine for rank = 1, 2 this is the error

message i get for rank = 3 and anything above that. Why is that ?

> BPnode<-CustomEndNodeList("GO:0008150",rank=3)

[1] "rank= 1"

[1] "rank= 2"

[1] "rank= 3"

Error in get(x, envir, mode, inherits) : variable "NA" was not found

Error in Ontology(get(id, env = GOTERM)) :

error in evaluating the argument 'object' in selecting a method for

function 'Ontology'

2. The other style i have use is to pass these nodes directly into 'endnode'


using endnode = c("GO:XXXXXX1","GO:XXXXXX2","GO:XXXXXX3",GO:XXXXXX4") and so


on. This seems to work, except that

(a) the final categories that are plotted are the top level categories among


those included in the endnode list. So say i had "immune response",
"response

to oxidative stress", "response to chemical stimulus" and "metabolic
process"

as my endnodes, my graph displays "biological_process", "metablolism"

and "unknown".

(b) I dont fully understand what is included in the "unknown" bars of the
plot.

Could someone please elaborate on this ?

(c) The last thing i found with sending in a user-defined endnode list is
that

the top ontology(ies) - BP, CC and MF are included by default. Sometimes, we


already know that we are looking at a specific ontology and there is no need


for it to be displayed on the barchart. I see that 3 top ontology GO terms
are

part of the code in ontoCompare and i tried re-defining this but was

unsuccessful.

Any ideas, help, suggestions would be greatly appreciated.

Regards,

Manasa Ramakrishna
Computational Biologist, Agresearch Limited, New Zealand

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