Hi Steve, This is not an error I've encountered before, so I don't know what the problem is off the top of my head. The error message makes me guess that the PWF is returning weird values (outside of the (0,1) range) for a couple of genes. Could you either send me the variables you used as input or try looking at the PWF p-values for the down list and see how they're distributed. If there's just a couple of values that are causing the problem, try changing them to NA, goseq will then treat them as "unknown length" and assign them a median weighting. If there are many with a nonsensical value I'll have to look at it more closely. Cheers, Matt On Sun, Oct 30, 2011 at 11:26 PM, steve Shen <shen.sq@gmail.com> wrote: > Hi Steve, > > Many thanks. It may be version unrelated. However, it handled the first > list perfectly. I can easily get terms with first list. However, the 2nd > and third lists are coming with errors. I assume there is limitation for > handling multiple .goWalls. You are right. I will wait the new R2.14 > release and to see what the diagnostics from Godon's group is. > > Best, > Steve > > On Sun, Oct 30, 2011 at 6:36 PM, Steve Lianoglou < > mailinglist.honeypot@gmail.com> wrote: > > > Hi, > > > > On Sun, Oct 30, 2011 at 6:10 PM, steve Shen <shen.sq@gmail.com> wrote: > > > Hi All, > > > > > > Using goSeq to analyze two gene lists - up regulated and down regulated > > > genes generated with edgeR, the up regulated list seems good, but there > > is > > > an error with down regulated list. Couldn't figure out what's wrong > with > > > it. Please refer to the command line and output below. Thanks very for > me > > > for help. > > > > Not sure what's wrong with it either, but your sessionInfo shows that > > you are using a (1) old version of R (2.12.1), and therefore (2) an > > old version of goseq. > > > > I would suggest upgrading to the newest R/Bioconductor/goseq combo to > > see if the error is still there. > > > > The slightly unfortunate thing for you is that R 2.14.0 is also > > scheduled to come out tomorrow so if you choose to upgrade to R > > 2.13.x, you will have the latest and greatest for < 24 hrs. The > > upgrade process isn't all that burdensome, so no big deal, but you > > might consider updating straight to the version of 2.14 that you can > > get from the link below as 2.14-branch: > > > > http://r.research.att.com/ > > > > > Steve > > > > You said it, brother. > > > > -- > > Steve Lianoglou > > Graduate Student: Computational Systems Biology > > | Memorial Sloan-Kettering Cancer Center > > | Weill Medical College of Cornell University > > Contact Info: http://cbio.mskcc.org/~lianos/contact > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Sorry, I meant PWF probabilities, not p-values. On Thu, Nov 3, 2011 at 8:25 AM, Matthew Young <myworkemailisnow@gmail.com>wrote: > Hi Steve, > > This is not an error I've encountered before, so I don't know what the > problem is off the top of my head. The error message makes me guess that > the PWF is returning weird values (outside of the (0,1) range) for a couple > of genes. Could you either send me the variables you used as input or try > looking at the PWF p-values for the down list and see how they're > distributed. If there's just a couple of values that are causing the > problem, try changing them to NA, goseq will then treat them as "unknown > length" and assign them a median weighting. If there are many with > a nonsensical value I'll have to look at it more closely. > > Cheers, > > Matt > > > On Sun, Oct 30, 2011 at 11:26 PM, steve Shen <shen.sq@gmail.com> wrote: > >> Hi Steve, >> >> Many thanks. It may be version unrelated. However, it handled the first >> list perfectly. I can easily get terms with first list. However, the 2nd >> and third lists are coming with errors. I assume there is limitation for >> handling multiple .goWalls. You are right. I will wait the new R2.14 >> release and to see what the diagnostics from Godon's group is. >> >> Best, >> Steve >> >> On Sun, Oct 30, 2011 at 6:36 PM, Steve Lianoglou < >> mailinglist.honeypot@gmail.com> wrote: >> >> > Hi, >> > >> > On Sun, Oct 30, 2011 at 6:10 PM, steve Shen <shen.sq@gmail.com> wrote: >> > > Hi All, >> > > >> > > Using goSeq to analyze two gene lists - up regulated and down >> regulated >> > > genes generated with edgeR, the up regulated list seems good, but >> there >> > is >> > > an error with down regulated list. Couldn't figure out what's wrong >> with >> > > it. Please refer to the command line and output below. Thanks very >> for me >> > > for help. >> > >> > Not sure what's wrong with it either, but your sessionInfo shows that >> > you are using a (1) old version of R (2.12.1), and therefore (2) an >> > old version of goseq. >> > >> > I would suggest upgrading to the newest R/Bioconductor/goseq combo to >> > see if the error is still there. >> > >> > The slightly unfortunate thing for you is that R 2.14.0 is also >> > scheduled to come out tomorrow so if you choose to upgrade to R >> > 2.13.x, you will have the latest and greatest for < 24 hrs. The >> > upgrade process isn't all that burdensome, so no big deal, but you >> > might consider updating straight to the version of 2.14 that you can >> > get from the link below as 2.14-branch: >> > >> > http://r.research.att.com/ >> > >> > > Steve >> > >> > You said it, brother. >> > >> > -- >> > Steve Lianoglou >> > Graduate Student: Computational Systems Biology >> > | Memorial Sloan-Kettering Cancer Center >> > | Weill Medical College of Cornell University >> > Contact Info: http://cbio.mskcc.org/~lianos/contact >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]