[BioC] Agilent Mouse 8x60K array

[James W. MacDonald]

I guess it depends on what you want to do with the positive and negative 
controls and the replicated stuff. I might be lacking vision here, but 
it seems to me there are only limited things that can be done. The only 
interesting things I have ever come up with are

Boxplots of different types of controls, by array.
Scatter plots of the spike-in controls. You could get fancy here and fit 
linear models and stuff, but I find that sort of boring and 
uninteresting. I just want to see that they look relatively similar 
after normalization.
Average replicates of non-controls, or maybe better - just use a single 
observation so you aren't smoothing.

I don't use the Agi4x44PreProcess package for any of that, because it is 
really simple to do by hand. Did you want to do something else?

Best,

Jim



On 2/4/2013 2:26 PM, Nathan (Nat) Goodman wrote:
> I've seen Agi4x44PreProcess, too.  As far as I can tell, it simply averages the replicas (!!??).  I'll look at it more deeply if you think it might do more.
>
> Best,
> Nat
>
> On Feb 4, 2013, at 11:16 AM, James W. MacDonald wrote:
>
>> Hi Nat,
>>
>> The Agi4x44PreProcess package does some things with the controls on the Agilent 4x44 array format, and you might look there for inspiration.
>>
>> Best,
>>
>> Jim
>>
>> On 2/4/2013 2:10 PM, Nathan (Nat) Goodman wrote:
>>> 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
>>>>>
>>>>>
>>>>> 	[[alternative HTML version deleted]]
>>>>>
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>>>> -- 
>>>> James W. MacDonald, M.S.
>>>> Biostatistician
>>>> University of Washington
>>>> Environmental and Occupational Health Sciences
>>>> 4225 Roosevelt Way NE, # 100
>>>> Seattle WA 98105-6099
>>>>
>> -- 
>> James W. MacDonald, M.S.
>> Biostatistician
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
>>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099