[BioC] normalization across sites

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Fri Jun 22 04:13:23 CEST 2007

Yes, you could do that.

What Sean is alluding to, is the fact that there is usually a large  
between-lab variation. Some times this variation is greater than the  
biological variation. If you are downloading from a website (or for  
that matter anyway) you should do proper QC of the chips, because you  
will have little idea of what the original people did with it and  
whether they made good choices.

In principle, if the hybes are good and you use proper normalization,  
hopefully you will get results that are comparable from lab to lab.  
But this is not at all given, and you need to be careful when you do  
these things.


On Jun 21, 2007, at 6:51 PM, Weiwei Shi wrote:

> Ok, if I understand correctly, I should combine two sources of data
> and run RMA on it?
> On 6/21/07, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>> Weiwei Shi wrote:
>>> Hi,
>>> Suppose that I have two sets of arrays, both of which use the same
>>> platform. My question is, if I have datasets which have been
>>> preprocessed, what's the best way for me to normalize them.  
>>> Currently
>>> I just scale them sample-wise; but not sure of it.
>>> Otherwise, should I go back to .CEL file? But how to proceed from  
>>> there?
>> Start from raw data, yes.  You may need to use an ANOVA or linear  
>> model
>> to deal with confounding variables.  Quality control is especially
>> important.
>> Sean
> -- 
> Weiwei Shi, Ph.D
> Research Scientist
> GeneGO, Inc.
> "Did you always know?"
> "No, I did not. But I believed..."
> ---Matrix III
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