[BioC] limma how to ignoring background

[Sean Davis]

On May 5, 2005, at 1:12 PM, M PEREZ wrote:

> Hi,
> I think that normalizeWithinArrays correct for background
> by default, so could be a good idea if you are going to do intrachip 
> normalization add this
> MA <- normalizeWithinArrays(RG.no.background, bg.method="none")
>

It may be my version of limma, but I don't have a bg.method as an 
option for normalizeWithinArrays.  In any case, RG.no.background 
contains no background information, so none will be used for 
normalization.

Sean


> Sean Davis <sdavis2 at mail.nih.gov> escribio:
> If RG is your RGList (from read.maimages), use:
>
>
> RG.no.background <- backgroundCorrect(RG,method='none')
>
> This will take out all background values so that they will not be used
> in further analysis.
>
> Sean
>
> On May 5, 2005, at 11:28 AM, Guoneng Zhong wrote:
>
>>
>> Hi,
>>
>> My custom image result files do not have background readings. But
>> limma's
>> read.maimages ask me for it. How do I get around this? I tried lying
>> to it by
>> giving it some random numeric column in the result file, but am
>> worried that
>> when I do normalization or lmFit it will take that fake background 
>> into
>> consideration.
>>
>> Any advice would be appreciated.
>>
>> Thanks,
>> g
>>
>> -- 
>>
>> Systems Programmer
>> Yale Center for Medical Informatics
>> fax: 203-737-5708
>>
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>
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