[BioC] normalization one color microarrays

[Sean Davis]

On Wed, Aug 24, 2011 at 5:12 PM, Laurent Gautier <laurent at cbs.dtu.dk> wrote:
> On 2011-08-24 23:04, Sean Davis wrote:
>>
>> On Wed, Aug 24, 2011 at 4:08 PM, Paz Tapia Ramirez
>> <verotapia at alumnos.utalca.cl>  wrote:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Hello, I am starting to work with ONE color microarrays from Agilent, and
>>> I read that during the pre-processing is main tasks, such as background
>>> adjustment, normalization and summarization. Currently I have corrected the
>>> background and  normalized samples, but do not understand the step of the
>>> summarization. Can you help me please?
>>>
>> Hi, Paz.
>>
>> For Agilent, there is not typically a summarization step (pulling
>> multiple probes into a "probe set").  Each probe is designed to
>> measure nucleotides independently.
>>
>> Sean
>>
>
> This depends on the use case, and what is typical to a lab might to an
> other.
> For custom arrays, I have seen a lot of designs with several probes per
> genes and there a probe summarization step could be applied.

Good point.

Sean

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