[BioC] help with affy st gene arrays

[Vincent Carey]

http://www.bioconductor.org/help/workflows/oligo-arrays/

gives a reasonably thorough discussion of relevant resources

On Thu, Nov 11, 2010 at 7:02 PM, Mark Cowley <m.cowley at garvan.org.au> wrote:
> 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
>>>>
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>>>
>>>
>>
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>
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