[BioC] doing some math on an array of PM probes

[Stuart Brown]

I would like to normalize probe signals per gene on a single Affy 
array by dividing
each pm probe by the mean of all pm probes on that array. Never mind 
that this is a
stupid thing to do, I have an idea...

The command  pm(affybatch)
gives a single probe value in each row and adds a numerical suffix to 
the gene name so
that each probe has a unique gene name.

Instead,  I'd like to extract the pm probes into a matrix that has a 
single Affy gene name for a row header and the signal values for all 
of the pm probes for that gene in the following columns of that row. 
Some genes will have different numbers of columns since they have 
different numbers of
pm probes. [If I could just get a table in this shape, I could 
actually do all the rest of the work
in Excel.]

Then I'd like to take the mean of all the probe signal values for 
each gene and write that into a new array that has just 2 rows - 
genename (which serves as the index) and mean-pm for that gene.

Finally, I'd like to replace the values of each pm probe signal with 
the ratio of that probe signal divided by  the mean of all pm probes 
for that gene.

There must be an easy way to do this, but I'm new to Bioconductor.

Thanks for any and all helpful suggestions
-Stuart Brown


-- 
Stuart M. Brown, PhD.
Associate Professor
Director, Research Computing Resource
NYU School of Medicine
550 First Ave, NY, NY 10016
stuart.brown at med.nyu.edu
(212)263-7689   FAX (212) 263-8139