[BioC] GOstats question

Sean Davis sdavis2 at mail.nih.gov
Wed Mar 30 17:37:41 CEST 2005

On Mar 30, 2005, at 10:19 AM, Rickman David wrote:
> I am new to the list and didn't see his posting --

I just meant that you could probably glean some detail from his note 
that I may have left out.  I am always deleting stuff that doesn't 
interest me at the moment, so I just meant to point out that the 
subject has come up....

> Even if the design (or the aim of the Bioconductor team) is limited to 
> a
> "general approach" which precludes working at the level of protein
> product (or transcript) -- which is the basis of the GO annotation and
> usually the goal of any test of GO category enrichment for a microarray
> result -- then for a given LL # we should have all available GO terms
> attributed, right? The example I gave showed that for at least two 
> probe
> sets (sharing the same LL #) this is not the case -- we have only 2 GO
> terms to work with versus 12 (again using the same reference GOA as a
> reference) for a well characterized gene.
> It looks like that is what it takes to get to core of the problem -- 
> One
> of my aims (I am sure like many using Affy data) is to summarize/study
> lists of probe sets derived from some test at the level of GO terms.
> Therefore it is almost intuitive that key to that aim is to resolve 
> both
> the multiplicity issues (many probe sets to one protein product,
> somewhat addressed in the GOstats package -- at the level of LocusLink)
> as well as the splice variant issues -- otherwise, it seems that
> analyses will always stay at a "general" level.

Just out of curiosity, I pulled down the most recent hgu133a annotation 
package.  I think your GO terms are there, so perhaps you have an older 
hgu133a package?

 > library(reposTools)
Loading required package: tools
 > install.packages2('hgu133a',lib='/Users/sdavis/Library/R/library')
 > library(annotate)
 > library(hgu133a)
 > names(get('207039_at',hgu133aGO))
  [1] "GO:0007049" "GO:0007049" "GO:0007050" "GO:0000075" "GO:0004861"
  [6] "GO:0016301" "GO:0045786" "GO:0008285" "GO:0005634" "GO:0000079"
 > names(get('211156_at',hgu133aGO))
  [1] "GO:0007049" "GO:0007049" "GO:0007050" "GO:0000075" "GO:0004861"
  [6] "GO:0016301" "GO:0045786" "GO:0008285" "GO:0005634" "GO:0000079"

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