[BioC] Batch effect

James W. MacDonald jmacdon at uw.edu
Wed Sep 5 15:10:17 CEST 2012

Hi Santana,

On 9/5/2012 2:14 AM, Santana Sarma wrote:
> Hi,
> How is it possible to judge whether there is any batch effect in two groups
> of Affymetrix .cel files ? I have got currently one Affybatch object by
> reading all the .cell files.

There are several things you can look at. I find PCA plots very helpful 
to look for batch effects. You might also look at density plots (hist() 
function in affy) as well as boxplots. But IMO PCA is the most useful.



> Being new to Affymetrix analysis, any advice/elaboration will be very
> helpful.
> Cheers,
> Santana
> 	[[alternative HTML version deleted]]
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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