[BioC] help with affy st gene arrays

[Mark Cowley]

Hi Yongde,
also take a look at the oligo package for normalizing your Gene ST arrays
cheers,
Mark
On 12/11/2010, at 8:51 AM, YBao wrote:

> Thanks so much, Achilleas, for the quick response. I will try to use
> those two packages and see how far I can go with them.
> 
> Yongde
> 
> On Thu, Nov 11, 2010 at 4:24 PM, Achilleas Pitsillides
> <anp4r at virginia.edu> wrote:
>> 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 at 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
>>> 
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> 
>> 
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor