[BioC] External expression data/ MAS5 Signal

Laurent Gautier laurent@cbs.dtu.dk
Thu, 13 Jun 2002 21:45:09 +0200

On Thu, Jun 13, 2002 at 10:34:46AM -0700, Peter Dimitrov wrote:
> On Thu, 2002-06-13 at 09:59, Rafael A. Irizarry wrote:
> > > #1. how can I import the external expression value table to affy? If
> > > possible, in which format?
> > what do you mean by external expression value table? if its just a flat 
> > file you can use read.table (an R command)
> > 
> > > #2. I saw AvgDiff, AvgDiff2, rma, and li.wong in express. Is it possible to
> > > calculate the Signal value which is implemented to Microarray Suite version
> > > 5 in affy?
> > > 
> > as far as i know the algorithm isnt public yet so we can't incorporate it.
> Can I propose a little change in express, that will accomodate
> background specific correction as in the case of MAS5. Specifically,
> parameter bg that is used to specify the background adjustment function,
> expects only functions that work on a chip or probe pair level, but not
> on a probeset level, such as MAS5. The thing is when the data comes to
> summary.stat, which is a function working on the probe level, the probe
> pairs are already reduced to single number and it is too late to apply
> MAS5. For more info look at
> http://www.stat.berkeley.edu/users/terry/zarray/Affy/affy_index.html

Dear Peter,

One can do what you describe using the method generateExprSet (for
objects of class Cel.container) of the version 1.1.x of the package
(in the devel section)... your comments are welcome if you have a
chance to look at it...



Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 85		http://www.cbs.dtu.dk/laurent