[BioC] problems running DEXseq

[Steve Lianoglou]

Hi,

On Sun, Jun 30, 2013 at 1:27 AM, Wolfgang Huber <whuber at embl.de> wrote:
> Dear Diya
>
> it appears that you are running dexseq_count.py as if it were a shell script, rather than from Python. As a consequence, the first line of the script is interpreted as the Linux command 'import' rather than as Python code, leading to the error you report.
>
> It also seems a bit troubling that you run this code as a superuser. That should never be necessary.
>
> Maybe best would be for you to hook up locally with a sys admin or with someone knowledgeable in Unix scripting, since it seems difficult to diagnose your particular system architecture remotely.

It's perhaps also worth mentioning that there is, I believe, a
completely "in R" method to do "proper" exon counting for DEXSeq
analysis that is outlined in the parathyroidSE data package vignette:

http://bioconductor.org/packages/release/data/experiment/vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf

-steve

--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech