[BioC] hgu133plus2 GO issues

[James W. MacDonald]

Jake wrote:
>>Here is the difference:
>>
>>hgu133plus2GO maps Probe IDs to GO terms
>>hgu133plus2GO2 PROBE maps GO terms to Probe IDs
>>hgu133plus2GO2ALLPROBES maps GO terms and all children of the terms to 
>>Probe IDs
> 
> 
> Thanks for the quick response, Jim. I just want to make sure that I'm
> understanding this correctly:
> 
> The "children" are more specific descriptions/functions of the "parent"
> node (right?).  So are you saying that even if an Affy Probe ID only has
> evidence for a given parent node, GO2ALLPROBES will also include
> connected children nodes for which there is no evidence for that Affy
> ID?

Nope, you have that backwards. GO2ALLPROBES maps GO terms to AffyIDs. So 
if you have a GO term, say phosphorylation, and there aren't any AffyIDs 
that map to that particular GOID, GO2PROBE won't list anything. However, 
if there is an AffyID that maps to protein phosphorylation, which is a 
child term of phosphorylation, then GO2ALLPROBES will list that AffyID 
when you do a get() on the phosphorylation GOID.

What you are talking about is the mapping in the hgu133plus2GO 
environment. In that case, if a given AffyID maps to e.g., 
phosphorylation, that is the only GOID that will be returned, not that 
term and all its children.

As an aside, please don't respond just to me. Keep things on the list so 
the questions/answers can be found by others.

HTH,

Jim
> 
> Thanks,
> 
> Jake
> 


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.