[BioC] affy normalization

[Matthew Hobbs]

Hi,

I have been wondering about how to do quantile normalization of affy data for 
which probe-level data is not available.  I found an answer in the mailing 
list archive (see below)  but I'm afraid I can't find the vignette referred 
to nor can I find any information about whatever function is wrapped by 
normalize.quantiles. Can someone please give me more specifics about where to 
look for help?  Basically I would like to know how (and if!) I can do 
quantile normalization of data which is stored e.g.  as an R matrix not an 
AffyBatch object. 

I appreciate any help - thanks!

Matthew

----------------------------------------------------------------------
Matthew Hobbs

Garvan Institute of Medical Research
384 Victoria St            Ph   : (02) 9295 8327
Darlinghurst                
http://www.garvan.org.au        email:  m.hobbs at garvan.org.au
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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
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-- 
> 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.