[BioC] goSeq error

[Steve Lianoglou]

Hi,

On Sun, Oct 30, 2011 at 6:10 PM, steve Shen <shen.sq at 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