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

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 at="" 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor This email message, including any attachments, is for th...{{dropped:2}}