[BioC] makecdfenv, bg.correct

[Justin Borevitz]

Hi Ben et al.

We're working  with new tiling arrays for Arabidopsis and drosophila.  We
can create a new cdfenv for the arrays and  would like  to read in new  .CEL
files to execute bg.correct and  normalize.quantiles.  We would like to mask
many features that are  not unique in the  genome and are considering using
the rm.extra option in read.affybatch.  How should this be specified?  Can
we feed a matrix of T/F of dim(array.size,array.size) for which features to
use?  How are these setting specified externally?

rm.mask = FALSE, rm.outliers = FALSE, rm.extra = FALSE

Another option we considered is to use bg.correct on a matrix of cel
intensities rather  than on an affy.batch, how could I call
bg.correct(matrixofCelintensities)?

Thanks,
Justin

-----
Justin Borevitz
Ecology and Evolution (CLSC 915E)
University of Chicago
1101 E. 57th St.
Chicago, IL 60637 USA
(773) 702-5948 office
(773) 834-4055 lab
borevitz at uchicago.edu
http://naturalvariation.org