On Wed, Sep 5, 2012 at 11:44 AM, Santana Sarma <aimanusarma@gmail.com>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.
>

Batch effect is generally come into consideration when you have data(.cel
files) from two different laboratories. And you  want to merge them.

>
>
> Being new to Affymetrix analysis, any advice/elaboration will be very
> helpful.
>

Limma has function for batch effect correction . You can go through that.
Here's is one link may it helps you.

https://stat.ethz.ch/pipermail/bioconductor/2007-August/018690.html

Regards
Reema Singh

>
>
> Cheers,
>
> Santana
>
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