[BioC] topGO "under-represented" GO terms?

[jiayu wen]

Dear all,

I am using topGO (elim) to find overrepresented GO terms (below is 3  
example output terms). I am confused with the output "significant" and  
"expected". So if "significant"  < "expected" (in the case of "  
cellular process" and "cellular metabolic proces") , does it mean the  
GO terms are "under-represented"? whereas if "significant"  <  
"expected" (cell cycle) means those terms are overrepresented? If so,  
does topGO always reports "under-represented" GO terms as well? or I  
completely misunderstand it...

Biological Process:
     GO.ID                             Term						Annotated	Significant	 
Expected	elim
     GO:0009987                 cellular process      			8686		42    
			 50.55		 2.1e-06
     GO:0007049                 cell cycle					278			5			1.62		0.00031
     GO:0044237                 cellular metabolic process	4985		19			 
29.01		0.01706

Could some one help me to explain it.
Thank you very much,

Jean


On Jul 15, 2009, at 1:22 PM, Stefanie Figura wrote:

> Dear all,
>
>
>
> I have some problems with the analysis of the HumanHT-12 Chip from  
> Illumina
> and hope somebody can help me.
>
>
>
> I have been analysing the data using the GenomeStudio Software until  
> now.
> Due to the fact, that some of the bead types are underrepresented on  
> the
> array, illumina implemented a so called “imputing function”. The  
> Techsupport
> told me that it would not make a big difference if the imputing  
> function is
> used or not.
>
> While comparing the results using both methods (no imputing vs  
> imputing), I
> found that the “imputing  function” leads to more than twice as many
> differentially expressed genes (167 vs 396).
>
>
>
> I was wondering, if there is any analog function or package  
> implemented in R
> & Bioconductor ?
>
>
>
> Any kind of advice is welcome.
>
> Thank you very much in advance!
>
>
>
> Kind regards,
>
> Stefanie
>
>
>
> ----------------------------------------------------------------------------
> ---
>
> Dipl.Chem. Stefanie Figura
>
> Leibniz-Institut für Arterioskleroseforschung
>
> Department Genetische Epidemiologie vaskulärer Erkrankungen
>
> Domagkstrasse 3
>
> 48149 Münster
>
> ----------------------------------------------------------------------------
> ---
>
>
>
>
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