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
> >
>
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>
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