[BioC] gProcessed Signal normalization using cyclic loess

[Wei Shi]

Dear Viritha:

	I think you can normalize the gProcessed signal directly.

	Also there are ~100 negative control genes on this microarray platform which might be useful for the background correction and normalization. The nec() function in limma can use these negative controls to perform a normexp background correction. After that, you will normalize your data using cyclic loess method or the quantile method.

	Hope this helps. 


Cheers,
Wei

On Dec 7, 2010, at 9:47 AM, Martin Morgan wrote:

> On 12/06/2010 01:44 PM, viritha kaza wrote:
>> Hi Group,
>> I am interested in performing normalization with the agilent data
>> -Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature
>> Number version).The gProcessed signal has been deposited as a series
>> matrix file in Geo. I wanted to know if one can directly normalize
>> gProcossed signal or need any other parameters from feature extraction
>> file before one can perform cyclic loess normalization?
>> Thank you in advance,
>> Viritha
> 
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