[BioC] replicates and low expression levels

[Laurent Gautier]

On Mon, Jun 02, 2003 at 11:17:26AM +0100, Claire Wilson wrote:
> >On Fri, May 30, 2003 at 05:28:45PM +0100, Crispin Miller wrote:

<much wisdom cut>

> 
> Hi,
> 
> Just to clarify a couple of points. This suggest to me that filtering of genes with low expression is required prior to normalization and I was just wondering in Bioconductor how this is achieved without the use of Present/Absent calls and following on from a later point

One should keep in mind the assumption behind many of the normalization
techniques: "most of the genes are not differentially expressed across the
experiments". Filtering before normalization/scaling should be done with
that in mind.
In the case of the "affy" pacakge (since you mention P/A),
the normalization is performed at the probe level (no need for P/A).


L.