Batch effect removal before merging microarray data sets

Question

[Vinay]

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

Answer 1

[Zhilong Jia]

boxplot can easily figure out it.

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