Yes. That is because a wrote a reply too quickly.  Sorry about that.

A fix that may work is the following:

options(verbose=TRUE)
PGSEA(....)

This may fix the problem in the short term.  We are currently working on a
permanent solution.

-kyle

  


On 2/25/08 1:43 PM, "Johan Lindberg" <johlin@kth.se> wrote:

> Hmm, unfortunately that didn't do much. 
> 
> My top candidate is still:
>   GO:0048806 genitalia development  1.314946e-98
>  
> Which has only 1 probe mapped to it according to:
>> > test <- contents(hsOligoGO2PROBE, all.names)
>> > test[5124]
> $`GO:0048806`
>          IMP 
> "Humv390D21"
> 
> My two commands are:
> 
> gseaGO <- go2smc(min = 10, max = 1000)
> pgsea.res = PGSEA(coefMatrix, cl=gseaGO, range = c(500, 1000), ref = NULL,
> center = FALSE, p.value = TRUE, weighted = TRUE, verbose=TRUE)
> 
> and then the pgsea.res just contains:
>> > names(pgsea.res)
> [1] "results"   "p.results"
> 
> that is, no extra output.
> 
> Other ideas?
> 
> Hmm, I think I can write a small function to filter out the GO-categories
> supported by few probes but I would be nice to have the bug corrected :)
> 
> Best regards
> 
> // Johan
> 
> On Feb 25, 2008, at 18:15 , Furge, Kyle wrote:
> 
>> The range option is *supposed* to work as you describe.
>> 
>> Unfortunately, there is a bug in the code. We have found the bug and are
>> working to fix it. We should have an updated version placed in the
>> development repository shortly.
>> 
>> In the mean time, a quick fix is to run the PGSEA function with the verbose
>> option set to TRUE (i.e. PGSEA(...,verbose=TRUE). While this will result in
>> some extra output, the range checking should work.
>> 
>> -kyle 
>> 
>> 
>> On 2/24/08 6:16 PM, "Johan Lindberg" <johlin@kth.se> wrote:
>> 
>>  
>>> 
>>> 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.
>>> 
>>>  
>>>> get("GO:0048806",hsOligoGO2PROBE)
>>>>         IMP
>>>> "Humv390D21"
>>>>  
>>> 
>>> 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
>>> unreliable?
>>> 
>>> Best regards
>>> 
>>> // Johan
>>> 
>>> _______________________________________________
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>>>  
>> 
>> 
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> 
>  
> ********************************************* 
> Johan Lindberg 
> Royal Institute of Technology 
> AlbaNova University Center 
> Stockholm Center for Physics, Astronomy and Biotechnology 
> School of Molecular Biotechnology 
> Department of Gene Technology 
> Visiting address: 
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> 106 91 Stockholm, Sweden 
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> 
>  
> 
> 



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