[BioC] Agilent Mouse 8x60K array

[James W. MacDonald]

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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