Microarray data processing from multiple runs

Question

[fanli.gcb]

Hi all,

Blast from the past here. I have some microarray data (looks like Affy HuEx) comprising 8 different chips/runs. Should I read each directory and perform RMA normalization separately, or put all the *.CEL files in a single directory and then do a single RMA call?

I'm not clear if the robust multi-array refers to multiple samples per chip or multiple chips.

Thanks!

Answer 1

[ATRX]

If they are from the same chip platform (or GPL id) then you may run all in the same run. However, you need to visualize the samples in PCA and see if it makes sense or not for ex: no Batch Effects. Robust multi-array can be used for data from different platforms like Affr Exon or Affy Gene but that does not mean that you can pool the data together and do normalization, since, the probes ids will be different.