[BioC] A questions related to affymetrix chip normalizationfrom multiple platform

[Li, Aiguo (NIH/NCI) [C]]

Hi Adai,

Thanks for getting back to me.  

I have about 100 HGU133A and HGUB and another 100 HGU plus2. I am sure
that I can normalize each set separately, then union all of them.  My
concern will be the batch effects within each set.  Can I do a secondary
normalization using some simple approach trying to remove the batch
effects among the sets?  
Thanks,

A.G. Lee



-----Original Message-----
From: Adaikalavan Ramasamy [mailto:ramasamy at cancer.org.uk] 
Sent: Wednesday, April 12, 2006 7:00 PM
To: Li, Aiguo (NIH/NCI) [C]
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] A questions related to affymetrix chip
normalizationfrom multiple platform

How many samples do you have with HGU133A, HGU133B and HGU133 plus 2.0 ?

You might have to preprocess the 3 different chip types separately and
then merge using union approach. This means that the samples from A and
B chip type would have missing values.

MAS 5.0 is outdated and has been shown to perform poorly for
low-abundance genes. Use RMA, GCRMA or some other modern algorithm.

Regards, Adai



On Tue, 2006-04-11 at 17:57 -0400, Li, Aiguo (NIH/NCI) [C] wrote:
> Hello all.
> 
>  
> 
> I have a set of chips using affymetrix platform.  Some of the chips
are
> from U133A and U133B and the others are plus2 chips.  As I understand,
> all the probesets in U133A and U133B are included in plus2 chips.  The
> question now is how I can normalize the cel files from 2 or 3
platforms.
> I saw people have used MAS-5 output with a common scaling factor, for
> example 500, for all platforms.  Is there a better way than that?  
> 
>  
> 
> Thanks in advance!
> 
>  
> 
> A.G. Lee
> 
> 
> 	[[alternative HTML version deleted]]
> 
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