[BioC] Gene expression data normalization question---batch effect related

[Sean Davis]

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