[BioC] Agilent Mouse 8x60K array

[Nathan (Nat) Goodman]

Thanks, Jim.  I am already using limma which does the basic processing quite well, but I don't think it does anything with the positive and negative controls or the numerous replicated non-control probes on the Agilent array.  I'm looking for a package that does something useful with these features.

Best,
Nat

On Feb 4, 2013, at 10:44 AM, James W. MacDonald wrote:

> Hi Nat,
> 
> On 2/4/2013 9:47 AM, Nathan (Nat) Goodman wrote:
>> Greetings- I have been unable to find a bioc package which does for the agilent Mouse 8x60K array, what the affy package does for affymetrix arrays.  Any pointers?
> 
> These Agilent arrays have a single 60-mer per transcript, so don't require something like the affy package (which is intended to summarize multiple 25-mers for a transcript to a single statistic). Instead, you most likely just need something like limma, which has the necessary functionality to read the data in, read in the GAL file so you annotate your output, normalize, and make comparisons.
> 
> The limma User's Guide has several Agilent examples, IIRC, so I would start there.
> 
> Best,
> 
> Jim
> 
> 
>> 
>> Many thanks,
>> Nat Goodman
>> ISB
>> 
>> 
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> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
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