[BioC] affy normalization

[Laurent Gautier]

On Tue, May 06, 2003 at 06:44:34PM +0200, David Rickman wrote:
> To whom it may concern,
> 
> i am very new to BioConductor and have a seemingly basic question.  How
> does one use the 7 different normalization techniques with affy data
> that is not in a CEL or AFFYBATCH format.  Essentially I have Avg.Diff.
> values of several U133A chips and would like to vis. and normal. using
> most of the tools found in your affy package.  The data is matrix form
> (text tab-delim. table) with probe names and Avg.Dif values for several
> samples.  I know this isn't ideal but i still wanted to take advantage
> of the strengths of you package.
> 
> any help would be greatly appreciated!!
> 
> David Rickman
> project leader
> Ligue Nationale Contre le Cancer
> France
> 

Each normalization method working on AffyBatch objects is a wrapper around
a another function dealing with matrices (to facilitate the port to other
classes (like marray*)) or for cases like yours.
Try the vignette about 'custom processing methods' for the naming
convention and refer to the individula normalizationmethods help pages.
For the visualization you may have to work the things by yourself...

Hopin' it helps,


L.


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Laurent Gautier			CBS, Building 208, DTU
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