[BioC] Tiling array application

James MacDonald jmacdon at med.umich.edu
Sat Apr 2 03:04:28 CEST 2005

It doesn't make any sense to use gcrma() if you don't have MM probes;
the idea behind gcrma is to come up with a better measure of background
than the MM measure itself. A modification of gcrma() that doesn't use
MM probes is rma().



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
>>> Shinhan Shiu <shiu at uchicago.edu> 04/01/05 5:13 PM >>>
We are trying to use GCRMA to adjust raw intensity values from tiling
experiments (Arabidopsis). But the affy Arabidopsis tiling chip do not
mismatch probes and it seems the mismatch probe intensity is absolutely 
required in:


Where the mismatch probe intensities, mismatch probe affinity, and
match probe affinities are passed. I wonder how this function can be 
modified so only perfect match probe info is used. Thanks.


  Shinhan Shiu
  Dept. of Ecology and Evolution
  University of Chicago

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