[BioC] Batch effect

[Wolfgang Huber]

Dear Santana

you could try the arrayQualityMetrics function in the eponymous package, 
which produces PCA plots and other diagnostics and is helpful to detect 
batch effects.

The function runs either on the AffyBatch object, or the normalised 
ExpressionSet; the former is more useful to understand how well the 
experiment worked, the latter, how well subsequent analyses might work.

	Best wishes
	Wolfgang


Sep/5/12 3:10 PM, James W. MacDonald scripsit:
> 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.
>
> Best,
>
> Jim
>
>
>>
>>
>> Being new to Affymetrix analysis, any advice/elaboration will be very
>> helpful.
>>
>>
>> Cheers,
>>
>> Santana
>>
>>     [[alternative HTML version deleted]]
>>
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>


-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber