Dear list, I have a question about gene expression data normalization which is related to batch effect. The dataset which I am interested appear to be collected in several batches. Apparently, these batches were generated at varied time points. So my question is that whether I should pull all arrays (cel files) together and normalize or I should normalize arrays within batch and then concatenate them into a single file. Thank you very much for your help! Sincerely, Allen [[alternative HTML version deleted]]

On Fri, Jun 27, 2008 at 8:05 AM, ss <affysnp at="" gmail.com=""> wrote: > Dear list, > > I have a question about gene expression data normalization which is > related to batch effect. > > The dataset which I am interested appear to be collected in several > batches. Apparently, these batches were generated at varied time > points. > > So my question is that whether I should pull all arrays (cel files) together > and normalize or I should normalize arrays within batch and then concatenate > them into a single file. You will generally need to normalize together unless you have an experimental design that allows you to account for batch effect. In any case, you will want to do some plots, perhaps unsupervised clustering, and good quality control before you can begin to address whether or not a batch effect exists. Sean