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
>> >
>>
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>>
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>

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