[BioC] RE: quantile normalization

[Remo Sanges]

On Aug 30, 2004, at 6:01 PM, Reimers, Mark (NIH/NCI) wrote:

> My opinion now is that we should normalize within
> tissue-of-origin, and then standardize raw data across tissues by 
> scaling to
> constant median. However I find that RMA (1.3) gives different numbers 
> when
> I separate out the normalize( cel.data ) process from estimation ( rma(
> normed.data , normalize=F)), compared with rma( cel.data).  Has anyone 
> else
> observed this?

Yes I observed the same think.

There are more changed genes when you normalize within tissue-of-origin
instead of rma(cel.data). Now the problem is to understand if this 
variability
is due to numerical of biological issue.

By the way if I well remember the first vignette of RMA suggested to 
normalize
data within sample-of-origin while the next suggested to do simply 
rma(cel.data).

Any comment?

Thanks

Remo