[BioC] normalizing 133 a and b

Rob Dunne Rob.Dunne at csiro.au
Thu Nov 6 02:18:14 MET 2003

HI list,

how are people normalizing 133a and b chips?

here is what I am doing.

1) bg.correct.rma2 (so this is per chip)
2) extract the pm values for all chips
3) for each pair (A and B) get the probes in common (168 genes)
  and make a linear correction factor to to correct the B chip.
4) adjust all the B chips to thir corresponding A chip 
5) put the data (A and B) in a matrix and 
do quantile normalization
6) this gives me the corrected probes, unfortunately some
are now negative so I add a slight fudge factor
7) I read the probes back into an AffyBatch object and get
expression values (medianpolish)

					does this sound reasonable?


Rob Dunne         Fax: +61 2 9325 3200     Tel: +61 2 9325 3263
CSIRO Mathematical and Information Sciences     +61 2 9325 3100
Locked Bag 17, North Ryde, New South Wales, Australia, 1670         
http://matilda.vu.edu.au/~dunne  Email: Rob.Dunne at csiro.au

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