[BioC] Possible to combine U133A&B Affy chip in one analysis?

Zaki Fadlullah zaki.fadlullah at carif.com.my
Mon Oct 1 11:15:48 CEST 2012

Hello gentle people,

As the topic suggests, would it be possible to combine data of U133A&B affy chip? and more importantly how...

The main objective is to find differently expressed genes, and to maximise the use of available data...as there are many papers I have read that conducted experiments on U133A&U133B chips (on the same sample set), however in their result/discussion sections the papers seems to show only one figure

In this particular paper that I am trying to understand how they found differently expressed genes from these two separate chips, they have a sample set (with 2 replicates each) on U133A and the same sample set (also with 2 replicates each) on U133B.

I would like to maximise the available data in from all chips and conduct the analysis. I am familiar on how to differently expressed each one separately using R (limma, affy), but would it be possible to combine expression value of these two chips?? 

I am assuming I would have to normalise them separately, but after that I am not quite sure what to do or if it is even possible.. 

Any help/ suggestions would be greatly appreciated

Many thanks

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