[BioC] PGSEA question

Johan Lindberg johlin at kth.se
Mon Feb 25 00:16:10 CET 2008

Dear all.

I have just started using PGSEA and I have a question.

When using the GO-terms as "concepts" the go-term GO:0048806,  
"genitalia development" becomes highly significant with a p of  
1.314946e-98. But if I look how many of my probes on my chip that map  
to this GO-term its just one.

 >         IMP

When I execute the PGSEA command I use:
pgsea.res = PGSEA(coefMatrix, cl=gseaGO, range = c(100, 1000), ref =  
NULL, center = FALSE, p.value = TRUE, weighted = TRUE)

I thought that the "range" argument would remove concepts with fewer  
probes mapping to it than the lower number given in range (in this  
case 100 probes). So how come that I still get the go-term GO:0048806  
in my results object (pgsea.res) since only one probe map o it.

My first thought was that fore some probes/genes all the geneontology  
terms that they map to arent in the GO2PROBE environment and that the  
probes are mapped to this go-term when doing the PGSEA (that is  
probes that map to child terms of GO:0048806). But >100?

Hmm, if I got this wrong, how do you filter out concepts/gene sets  
supported by few probes on the chip since these groups are more  

Best regards

// Johan

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