[rmaexpress_help] Batch effect produced when using RMA

Hi Dr. Bolstad,

I have a question regarding how to use RMA correctly.
We have data of 120 microarrays. But those 120 microarrays were not done all together at one time. Actually, we collected 40 samples every time and then went ahead to do microarrays on those 40 samples. So basically we have 3 batches of microarrays (microarrays from the same batch were done at the same time and there was a gap of several months between two batches). I wonder in this case, when I use RMA, whether I should analyze those 120 microarrays together or I should analyze each batch of microarrays separately. I don't know the details of RMA, so I really don't know which way I should take.
I have tried to use RMA to analyze each batch of microarrays separately and then combined them together. I used PCA (principal component analysis) to do an unsupervised analysis and what I found was that the first principal component could perfectly separate three batches. I guess that means there is an obvious batch effect in the data after RMA. 

Look forward to getting your suggestions! Thanks a lot!

Jun

----------------------------
Jun Ding, Ph.D. student
Department of Biostatistics
University of Michigan
Ann Arbor, MI, 48105
----------------------------

Other related posts: