Hi Yongde,

I am no expert but for the last  Human Gene 1.0 ST array data I analyzed I
used the xps package for pre-processing and then to assess differential
expression I used the limma package. I am sorry I don't have any screenshots
but both packages have nice documentation in their vignettes, which should
be really straight forward to follow.

cheers,
Achilleas



On Thu, Nov 11, 2010 at 3:46 PM, YBao <yb8d@virginia.edu> wrote:

> Dear BioConductor experts,
>
>
> I wonder if anyone would be generous enough to share some
> scripts/screen images they use to analyze Affy ST gene arrays, either
> for human or mouse. I am particularly interested in learning what
> packages they use and what the output files look like.
>
> Thanks much,
>
>
>
> Yongde
>
> Dept. Microbiology
> University of Virginia
>
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