Question: Batch effect removal before merging microarray data sets
1
gravatar for Vinay
4.3 years ago by
Vinay30
India
Vinay30 wrote:

Hi, 

I know that expression data generated by different experiments cannot be combined directly for downstream analysis due to “batch-effects”. My question is very straight forward. Is batch effect removal necessary before merging normalized microarray datasets that use the same Affymetrix platform but different chip types, say HG-U133A and HG-U133PLUS2. Or simple merging can solve the purpose?

All kind suggestions will be appreciated.

Thanks.

microarray • 2.1k views
ADD COMMENTlink modified 4.3 years ago by Zhilong Jia1.4k • written 4.3 years ago by Vinay30
2
gravatar for Zhilong Jia
4.3 years ago by
Zhilong Jia1.4k
London
Zhilong Jia1.4k wrote:

boxplot can easily figure out it.

you can use combat (http://www.bu.edu/jlab/wp-assets/ComBat/Abstract.html)

ADD COMMENTlink written 4.3 years ago by Zhilong Jia1.4k
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