[BioC] Merging microarray datasets

[Robert Gentleman]

Hi Kathy,
   This question has been asked many times, and the advice remains the 
same: it doesn't make any sense to normalize different data sets 
together.  You should normalize them separately and use appropriate 
statistical models to combine the data into a single analysis.

best wishes
   Robert


Kathy Duncan wrote:
> Hi,
> 
> I have a simple and basic question:
> 
> Is it alright to think of merging two datasets (either from cDNA or
> Affymetrix platform) - Final goal is to have ONE normalized dataset, where
> the datasets are scaled in order to compensate the different types of
> variations, if present !
> 
> Comments on strategy and packages available in Bioconductor would be of
> great help.
> 
> Thanks.
> 
> Kathy
> 
> 
> * PS: Thanks James for your earlier reply (SORRY for the delay). Here, I
> have re-framed my question - I'm not sure *MergeMaid* exactly does what I'm
> looking for.
> 
> 
> = = == = =  = = = = =  = = =
> 
> 
> On Tue, Apr 15, 2008 at 1:19 AM, James W. MacDonald <jmacdon at med.umich.edu>
> wrote:
> 
>> Hi Kathy,
>>
>> Assuming the chips are all the same species, I would probably use
>> something like MergeMaid. There may be others -- you can check here:
>>
>> http://bioconductor.org/packages/2.2/DifferentialExpression.html
>>
>> Best,
>>
>> Jim
>>
>>
> 
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> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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PO Box 19024
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206-667-7700
rgentlem at fhcrc.org