[BioC] qspline Normalization

Paul Boutros pcboutro@engmail.uwaterloo.ca
Thu, 17 Oct 2002 14:51:09 -0400 (EDT)

Hi all,

I'd like to use the qspline normalization method:
normalize.celfile.qspline {affy}

I have two problems with this:
a) I would like to use this normalization on cDNA data.  Am I correct in
interpreting that this method can either be fun directly on a
Cel.container object, or alternately can be called a data.matrix of
intensity values and a target vector?  Or do I need to do something in
addition to use it for non-Affy data?

b) I am a bit unclear on some of the arguments, and I am unsure how to
pick appropriate levels.  In particular, I am unclear about how to
determine realistic values for:

Any advice or ideas would be very much appreciated.  And if this isn't the
right place for these questions, guidance on where to go would also be