[BioC] is-normalisation-really-required

[Sean Davis]

On Apr 12, 2005, at 1:19 PM, vijayaraj nagarajan wrote:

> dear friends
> i have situation, where i thought its ok for me not to
> do normalisation, i am afraid i may be wrong. i want
> your advice in this regard.
>
> we performed a wild type - mutant, dye-swap
> experiment.
> when we analysed the intensity values, they were
> consistant among the two experiment (dye-swap). ie.,
> almost same values for mutants in both the experiments
> of the dye-swap.
> since the values are almost same, i thought there
> might not be any dye-bias, so i just went ahead,
> averaged the two values, found out their ratio and
> filtered genes with 2 fold change.
>

If you don't normalize, then the "center" of your ratios may be 
significantly off, not to mention the fact that the two arrays may have 
different centers.  So, at the very least, I think you have to do 
within-arrays normalization of some kind.

Sean